Changelog (Released)¶

All notable user-facing changes to WEBKNOSSOS are documented in this file. See CHANGELOG.unreleased.md for the changes which are not yet part of an official release.

The format is based on Keep a Changelog and this project adheres to Calendar Versioning 0Y.0M.MICRO. For upgrade instructions, please check the migration guide.

24.12.0 - 2024-12-05¶

Commits

Added¶

When exploring remote URIs pasted from Neuroglancer, the format prefixes like precomputed:// are now ignored, so users don’t have to remove them. #8195

Changed¶

Reading image files on datastore filesystem is now done asynchronously. #8126
Improved error messages for starting jobs on datasets from other organizations. #8181
Terms of Service for Webknossos are now accepted at registration, not afterward. #8193
Removed bounding box size restriction for inferral jobs for super users. #8200
Improved logging for errors when loading datasets and problems arise during a conversion step. #8202

Fixed¶

Fixed performance bottleneck when deleting a lot of trees at once. #8176
Fixed a bug where changing the color of a segment via the menu in the segments tab would update the segment color of the previous segment, on which the context menu was opened. #8225
Fixed a bug when importing an NML with groups when only groups but no trees exist in an annotation. #8176
Fixed a bug where trying to delete a non-existing node (via the API, for example) would delete the whole active tree. #8176
Fixed a bug where dataset uploads would fail if the organization directory on disk is missing. #8230

Removed¶

Removed Google Analytics integration. #8201

24.11.1 - 2024-11-13¶

Commits

Highlights¶

It is now possible to add metadata in annotations to Trees and Segments. #7875
Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. #8123

Added¶

It is now possible to add metadata in annotations to Trees and Segments. #7875
Added a summary row to the time tracking overview, where times and annotations/tasks are summed. #8092
Most sliders have been improved: Wheeling above a slider now changes its value and double-clicking its knob resets it to its default value. #8095
It is now possible to search for unnamed segments with the full default name instead of only their id. #8133
Increased loading speed for precomputed meshes. #8110
Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. #8123
Unified wording in UI and code: “Magnification”/“mag” is now used in place of “Resolution“ most of the time, compare terminology document. #8111
Added support for adding remote OME-Zarr NGFF version 0.5 datasets. #8122
Workflow reports may be deleted by superusers. #8156

Changed¶

Some mesh-related actions were disabled in proofreading-mode when using meshfiles that were created for a mapping rather than an oversegmentation. #8091
Admins can now see and cancel all jobs. The owner of the job is shown in the job list. #8112
Migrated nightly screenshot tests from CircleCI to GitHub actions. #8134
Migrated nightly screenshot tests for wk.org from CircleCI to GitHub actions. #8135
Thumbnails for datasets now use the selected mapping from the view configuration if available. #8157

Fixed¶

Fixed a bug during dataset upload in case the configured datastore.baseFolder is an absolute path. #8098 #8103
Fixed bbox export menu item #8152
When trying to save an annotation opened via a link including a sharing token, the token is automatically discarded in case it is insufficient for update actions but the users token is. #8139
Fix that scrolling in the trees and segments tab did not work while dragging. #8162
Fixed that uploading a dataset which needs a conversion failed when the angstrom unit was configured for the conversion. #8173
Fixed that the skeleton search did not automatically expand groups that contained the selected tree #8129
Fixed interactions in the trees and segments tab like the search due to a bug introduced by #8162. #8186
Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. #8116
Fixed sorting of mags in outbound zarr streaming. #8125
Fixed a bug where you could not create annotations for public datasets of other organizations. #8107
Users without edit permissions to a dataset can no longer delete sharing tokens via the API. #8083
Fixed downloading task annotations of teams you are not in, when accessing directly via URI. #8155
Removed unnecessary scrollbars in skeleton tab that occurred especially after resizing. #8148
Deleting a bounding box is now possible independently of a visible segmentation layer. #8164
S3-compliant object storages can now be accessed via HTTPS. #8167
Fixed that skeleton tree nodes were created with the wrong mag. #8185
Fixed the expected type of a tree node received from the server. Fixes nml export to include the inMag field correctly. #8187
Fixed a layout persistence bug leading to empty viewports, triggered when switching between orthogonal, flight, or oblique mode. #8177

Removed¶

Breaking Changes¶

24.10.0 - 2024-09-24¶

Commits

Highlights¶

It is now possible to focus a bounding box in the bounding box tab by clicking its edges in a viewport or via a newly added context menu entry. #8054
Clicking on a bounding box within the bounding box tab centers it within the viewports and focuses it in the list. #8049

Added¶

Added the option to export nd datasets as ome tiff or tiff stack. Previously, this was only possible for 3d datasets. #7971
Added an assertion to the backend to ensure unique keys in the metadata info of datasets and folders. #8068
The feature to register all segments within a bounding box now takes the current magnification into consideration, e.g. for calculating the volume limit for a bounding box. #8082

Changed¶

For self-hosted versions, the text in the dataset upload view was updated to recommend switching to webknossos.org. #7996
Updated frontend package management to yarn version 4. 8061
Updated React to version 18. Updated many peer dependencies including Redux, React-Router, antd, and FlexLayout. #8048
Improved the performance of context menus in the bounding box tab. #8059

Fixed¶

The JS API v2 has been removed as it was deprecated by v3 in 2018. Please upgrade to v3 in case your scripts still use v2. #8076
Fixed that the precompute-meshfile button did not work in the segments tab. #8077
Removed the superfluous _type field when writing zarr3 codec jsons.

Removed¶

Breaking Changes¶

24.08.1 - 2024-09-03¶

Commits

Added¶

If the opacity of a volume layer is zero, a warning is now shown in the layer settings tab. #8003

24.08.0 - 2024-09-02¶

Commits

Highlights¶

The AI-based Quick Select can now be run on multiple sections at once. This can be configured in the tool settings. Also, the underlying model now uses Segment Anything 2. #7965
Metadata entries can now be added to datasets and folders. The metadata can be viewed and edited in the dashboard in the right details tab. #7886
The AI-based Quick Select can now be triggered with a single click. Drawing a rectangle is still supported. #7993
Added the option to resume an unfinished upload even after browser restarts. #7981
Added a feature to register all segments for a given bounding box at once via the context menu of the bounding box. #7979

Added¶

WEBKNOSSOS now automatically searches in subfolder / sub-collection identifiers for valid datasets in case a provided link to a remote dataset does not directly point to a dataset. #7912
Added the option to move a bounding box via dragging while pressing ctrl / meta. #7892
Added route /import?url=<url_to_datasource> to automatically import and view remote datasets. #7844
Added that newly created, modified and clicked on bounding boxes are now highlighted and scrolled into view, while the bounding box tool is active. #7935
The configured unit in the dataset upload view is now passed to the convert_to_wkw worker job. #7970
Added option to expand or collapse all subgroups of a segment group in the segments tab. #7911
The context menu that is opened upon right-clicking a segment in the dataview port now contains the segment's name. #7920
Upgraded backend dependencies for improved performance and stability. #7922
Added Support for streaming datasets via Zarr version 3. #7941
It is now saved whether segment groups are collapsed or expanded, so this information doesn't get lost e.g. upon page reload. #7928
It is now saved whether skeleton groups are collapsed or expanded. This information is also persisted to NML output. #7939
The context menu entry "Focus in Segment List" expands all necessary segment groups in the segments tab to show the highlighted segment. #7950
In the proofreading mode, you can enable/disable that only the active segment and the hovered segment are rendered. #7654
Upgraded s3 client for improved performance when loading remote datasets. #7936
The performance of the bounding box tab was improved. #7974
Added support for reading zstd-compressed zarr2 datasets #7964
The alignment job is in a separate tab of the "AI Tools" now. The "Align Sections" AI job now supports including manually created matches between adjacent section given as skeletons. #7967
Added api.tracing.createNode(position, options) to the front-end API. #7998
Added links in the workflow report for skipped tasks to the corresponding workflow view. #8006
Upgraded backend dependencies for improved performance and stability, including a memory leak fix for FossilDB. #8014

Changed¶

Replaced skeleton tab component with antd's <Tree />component. Added support for selecting tree ranges with SHIFT. #7819
The warning about a mismatch between the scale of a pre-computed mesh and the dataset scale's factor now also considers all supported mags of the active segmentation layer. This reduces the false posive rate regarding this warning. #7921
It is no longer allowed to edit annotations of other organizations, even if they are set to public and to others-may-edit. #7923
When proofreading segmentations, the user can now interact with super-voxels directly in the data viewports. Additionally, proofreading is significantly faster because the segmentation data doesn't have to be re-downloaded after each merge/split operation. #7654
Changed internal data model changing an organization's name to id and its displayName to name. The previously existing id was removed. #7386
Because of the way our models are trained, AI analysis and training is disabled for 2D and ND datasets, as well as for color layers with data type uInt24. #7957
The overall performance was improved (especially for the segments tab). #7958
The performance for the skeleton tab was improved. #7989
Upgraded ant icons to version 5.4. #8007
Increased maximum depth for ai-based quick select from 5 to 16. #8021
Zarr-streaming now uses the new unit-aware voxel size. This means that wk-libs client v0.14.25 or newer is needed for dataset zarr streaming. #8012
Updated React to version 17. #7765

Fixed¶

Fixed a bug that allowed the default newly created bounding box to appear outside the dataset. In case the whole bounding box would be outside it is created regardless. #7892
Fixed a rare bug that could cause hanging dataset uploads. #7932
Fixed that comments of the active tree were not scrolled into view in some cases when switching to the comments tab. 8022
Fixed that trashcan icons to remove layers during remote dataset upload were floating above the navbar. #7954
Fixed that the flood-filling action was available in the context menu although an editable mapping is active. Additionally volume related actions were removed from the context menu if only a skeleton layer is visible. #7975
Fixed that activating the skeleton tab would always change the active position to the active node. #7958
Made the newly added filePaths argument of the reserve upload route (see #7981) optional to be backwards compatible with wklibs. #8045
Fixed that skeleton groups couldn't be collapsed or expanded in locked annotations. #7988
Fixed that the dashboard didn't notify the user about new datasets in the table. #8025
Fixed that registering segments for a bounding box did only work if the segmentation had mag 1. #8009
Fixed uploading datasets in neuroglancer precomputed and n5 data format. #8008
Various fixes for composing datasets with landmarks. Note that the interpretation of correspondence points was inverted for thin plate splines. #7992

24.07.0 - 2024-07-05¶

Commits

Highlights¶

Owners can lock explorative annotations now. Locked annotations cannot be modified by any user. An annotation can be locked in the annotations table and when viewing the annotation via the navbar dropdown menu. #7801
Added the ability to change the unit of the dataset voxel size to any supported unit of the ome/ngff standard. This allows users to upload and work with low-resolution datasets with a different base unit than nanometer. #7783

Added¶

Added that proofreading merge actions reuse custom names of segments. A merge action now combines the potential existing custom names of both segments and a split-action copies the custom name to the split-off segment. #7877
Added the option to set a default mapping for a dataset in the dataset view configuration. The default mapping is loaded when the dataset is opened and the user / url does not configure something else. #7858
Uploading an annotation into a dataset that it was not created for now also works if the dataset is in a different organization. #7816
When downloading + reuploading an annotation that is based on a segmentation layer with active mapping, that mapping is now still selected after the reupload. #7822
In the Voxelytics workflow list, the name of the WEBKNOSSOS user who started the job is displayed. #7794
Start an alignment job (aligns the section in a dataset) via the "AI Analysis" button (not available to all users yet). #7820
Added additional validation for the animation job modal. Bounding boxes must be larger then zero. #7883

Changed¶

The "WEBKNOSSOS Changelog" modal now lazily loads its content potentially speeding up the initial loading time of WEBKNOSSOS and thus improving the UX. #7843
Updated the min / max settings for the histogram to allow floating point color layers to have negative min / max values. #7873
Made the login, registration, forgot password and dataset dashboard pages more mobile friendly. #7876
From now on only project owner get a notification email upon project overtime. The organization specific email list overTimeMailingList was removed. #7842
Replaced skeleton comment tab component with antd's <Tree />component. #7802
Updated Typescript to version 5.5.0. #7878

Fixed¶

Fixed a bug where the warning to zoom in to see the agglomerate mapping was shown to the user even when the 3D viewport was maximized and no volume data was shown. #7865
Fixed a bug that prevented saving new dataset settings. #7903
Fixed that on large screens the login forms were not horizontally centered. #7909
Fixed a bug where brushing on a fallback segmentation with active mapping and with segment index file would lead to failed saves. #7833
Fixed a bug where the "Hide Meshes" / "Show Meshes" options of the context menu for segment groups were not available although at least one mesh was set to visible / invisible. #7890
Fixed a bug where sometimes old mismatching javascript code would be served after upgrades. #7854
Fixed a bug where dataset uploads of zipped tiff data via the UI would be rejected. #7856
Fixed a bug with incorrect validation of layer names in the animation modal. #7882
Fixed a bug in the fullMesh.stl route used by the render_animation worker job, where some meshes in proofreading annotations could not be loaded. #7887
Fixed that dataset composition did not work when selecting only one dataset for composition. #7889

Removed¶

REST API versions 1 and 2 are no longer supported. Current is 7. #7783
If the datasource-properties.json file for a dataset is missing or contains errors, WEBKNOSSOS no longer attempts to guess its contents from the raw data. Exploring remote datasets will still create the file. #7697

24.06.0 - 2024-05-27¶

Commits

Highlights¶

Within the proofreading tool, the user can now interact with the super voxels of a mesh in the 3D viewport. For example, this allows to merge or cut super voxels from another. As before, the proofreading tool requires an agglomerate file. #7742
In the time tracking view, all annotations and tasks can be shown for each user by expanding the table. The individual time spans spent with a task or annotating an explorative annotation can be accessed via CSV export. The detail view including a chart for the individual spans has been removed. #7733

Added¶

Minor improvements for the timetracking overview (faster data loading, styling). #7789
Updated several backend dependencies for optimized stability and performance. #7782
Voxelytics workflows can be searched by name and hash. #7790
If a self-hosted WEBKNOSSOS instance has not been updated for six months or more, a closable banner proposes an upgrade to webknossos.org. #7768

Changed¶

Non-admin or -manager users can no longer start long-running jobs that create datasets. This includes annotation materialization and AI inferrals. #7753
The config value datastore.localFolderWhitelist can now be set for each datastore individually. #7800

Fixed¶

Fixed a bug where a toast that was reopened had a flickering effect during the reopening animation. #7793
Fixed a bug where some annotation times would be shown double. #7787
Fixed a bug where no columns were shown in the time tracking overview. #7803
Fixed a bug where ad-hoc meshes for coarse magnifications would have gaps. #7799
Fixed that the context menu didn't open correctly in the 3D viewport when right-clicking a node. #7809
Fixed that right-clicking a mesh in the 3D viewport did crash when the corresponding segmentation layer was not visible. #7811

24.05.0 - 2024-04-29¶

Commits

Highlights¶

Changed the time-tracking overview to show times spent in annotations and tasks and filter them by teams and projects. In the linked detail view, the tracked times can also be filtered by type (annotations or tasks) and project. #7524
Time Tracking now also works when editing other users’ shared annotations, and when editing proofreading annotations (a.k.a. editable mappings). #7749
Creating and deleting edges is now possible with ctrl+(alt/shift)+leftclick in orthogonal, flight and oblique mode. Also, the flight and oblique modes allow selecting nodes with leftclick, creating new trees with 'c' and deleting the active node with 'del'. #7678

Added¶

Added Typescript definitions for @scalableminds/prop-types package. #7744
Added Typescript definitions for react-remarkable package. #7748

Changed¶

Improved task list to sort tasks by project date, add option to expand all tasks at once and improve styling. #7709
The time tracking api route /api/users/:id/loggedTime, which is used by the webknossos-libs client, and groups the times by month, now uses UTC when determining month limits, rather than the server’s local timezone. #7524
Duplicated annotations are opened in a new browser tab. #7724
When proofreading segments and merging two segments, the segment item that doesn't exist anymore after the merge is automatically removed. #7729
Changed some internal APIs to use spelling dataset instead of dataSet. This requires all connected datastores to be the latest version. #7690
Toasts are shown until WEBKNOSSOS is running in the active browser tab again. Also, the content of most toasts that show errors or warnings is printed to the browser's console. #7741
Improved UI speed when editing the description of an annotation. #7769
Updated dataset animations to use the new meshing API. Animitation now support ad-hoc meshes and mappings. #7692

Fixed¶

Fixed that the Command modifier on MacOS wasn't treated correctly for some shortcuts. Also, instead of the Alt key, the ⌥ key is shown as a hint in the status bar on MacOS. #7659
Moving from the time tracking overview to its detail view, the selected user was not preselected in the next view. #7722
Fixed incorrect position of WEBKNOSSOS logo in screenshots. #7726
Fixed that invisible nodes could be selected when using the skeleton tool. #7732
Fixed a bug where users that have no team memberships were omitted from the user list. #7721
Added an appropriate placeholder to be rendered in case the timetracking overview is otherwise empty. #7736
The overflow menu in the layer settings tab for layers with long names can now be opened comfortably. #7747
Fixed a bug where segmentation data looked scrambled when reading uint32 segmentation layers with CompressedSegmentation codec. #7757
Fixed a bug when downsampling a volume annotation that previously had only a restricted magnification set. #7759

Removed¶

Meshfiles with version 2 or older are no longer supported. Talk to us about support in converting your old meshfiles. #7764

Breaking Changes¶

When merging two trees or segments, the active item will always "survive" the merge operation (the clicked item will be merged into the active one). This was not consistent for certain skeleton-based operations (i.e., merging skeletons with a shortcut and proofreading segmentations with agglomerate skeletons). #7729

24.04.0 - 2024-03-25¶

Commits

Highlights¶

Segment statistics are now available for ND datasets. #7411
Added a new "Split from all neighboring segments" feature for the proofreading mode. #7611
Added support for uploading N5 and Neuroglancer Precomputed datasets. #7578

Added¶

Added support for storing analytics events in the Postgres. #7594 #7609
Webknossos can now open ND Zarr datasets with arbitrary axis orders (not limited to **xyz anymore). #7592
Added support for skeleton annotations within datasets that have transformed layers. The skeleton nodes will move according to the transforms when rendering a specific layer natively. Also, downloading visible trees can be done by incorporating the current transforms. However, note that the back-end export does not take transforms into account. #7588
If storage scan is enabled, the measured used storage is now displayed in the dashboard’s dataset detail view. #7677
Prepared support to download full stl meshes via the HTTP api. #7587
You can now place segment index files with your on-disk segmentation layers, which makes segment stats available when viewing these segmentations, and also when working on volume annotations based on these segmentation layers. #7437
Added an action to delete erroneous, unimported datasets directly from the dashboard. #7448
Added support for window, active, inverted keys from the omero info in the NGFF metadata. 7685
Added getSegment function to JavaScript API. Also, createSegmentGroup returns the id of the new group now. #7694
Added support for importing N5 datasets without multiscales metadata. #7664

Changed¶

Datasets stored in WKW format are no longer loaded with memory mapping, reducing memory demands. #7528
Content Security Policy (CSP) settings are now relaxed by default. To keep stricter CSP rules, add them to your specific application.conf. #7589
The state of whether a mapping is active and what exact mapping is now locked to the annotation upon the first volume annotation action to ensure future consistent results. Moreover, while a JSON mapping is active, no volume annotation can be done. #7549
WEBKNOSSOS now uses Java 21. #7599
Email verification is disabled by default. To enable it, set webKnossos.user.emailVerification.activated to true in your application.conf. #7620 #7621
Added more documentation for N5 and Neuroglancer precomputed web upload. #7622
Added the config key webKnossos.user.timeTrackingOnlyWithSignificantChanges, which when set to true will only track time if the user has made significant changes to the annotation. #7627
Only display UI elements to launch background jobs if the (worker) backend actually supports them. #7591
If the current dataset folder in the dashboard cannot be found (e.g., because somebody else deleted it), the page navigates to the root folder automatically. #7669
Voxelytics logs are now stored by organization name, rather than id, in Loki. This is in preparation of the unification of these two concepts. #7687
Using a segment index file with a different data type than uint16 will now result in an error. #7698
Improved performance of JSON mappings in preparation of frontend HDF5 mappings. #7706
Removed remaining ESLint configuration files and replaced circular dependency detection tool from madge to dpdm. #7743

Fixed¶

Fixed rare SIGBUS crashes of the datastore module that were caused by memory mapping on unstable file systems. #7528
Fixed loading local datasets for organizations that have spaces in their names. #7593
Fixed a bug where proofreading annotations would stay black until the next server restart due to expired but cached tokens. #7598
Fixed a bug where ad-hoc meshing didn't make use of a segment index, even when it existed. #7600
Fixed a bug where importing remote datasets with existing datasource-properties.jsons would not properly register the remote credentials. #7601
Fixed a bug in ND volume annotation downloads where the additionalAxes metadata had wrong indices. #7592
Fixed a bug in proofreading aka editable mapping annotations where splitting would sometimes give the new id to the selected segment rather than to the split-off one. #7608
Fixed small styling errors as a follow-up to the antd v5 upgrade. #7612
Fixed that the iOS keyboard automatically showed up when moving through a dataset. #7660
Fixed deprecation warnings caused by Antd \<Collapse> components. #7610
Fixed small styling error with a welcome notification for new users on webknossos.org. #7623
Fixed that filtering by tags could produce false positives. #7640
Fixed a slight offset when creating a node with the mouse. #7639
Fixed small styling error with NML drag and drop uploading. #7641
Fixed a bug where the annotation list would show teams the annotation is shared with multiple times. #7659
Fixed incorrect menu position that could occur sometimes when clicking the ... button next to a segment. #7680
Fixed an error in the Loki integration to support Loki 2.9+. #7684
Fixed inconsistent style of antd components and odd behavior of dataset/annotation description Markdown input. #7700

Removed¶

Removed the integration with BrainTracing user databases. #7693

Breaking Changes¶

Updated antd UI library from version 4.24.15 to 5.13.2. Drop support for nodeJs version <18. #7522

24.02.3 - 2024-02-22¶

Commits

Fixed¶

Fixed a bug where the user list view would show duplicate team roles, and user changes (e.g. giving experience) would sometimes fail. #7646

24.02.2 - 2024-02-15¶

Commits

Fixed¶

Fixed a bug where the annotation list in the dashboard would attempt to display deleted annotations, and then fail. #7628

24.02.1 - 2024-02-15¶

Commits

Fixed¶

Fixed a bug where the annotation list in the dashboard would attempt to display deleted annotations, and then fail. #7628

24.02.0 - 2024-01-26¶

Commits

Highlights¶

Added thumbnails to the dashboard dataset list. #7479
The data of segments can now be deleted in the segment side panel. #7435
Added the ability to compose a new dataset from existing dataset layers. This can be done with or without transforms (transforms will be derived from landmarks given via BigWarp CSV or WK NMLs). #7395

Added¶

Added support for S3-compliant object storage services (e.g. MinIO) as a storage backend for remote datasets. #7453
Added support for blosc compressed N5 datasets. #7465
Added route for triggering the compute segment index worker job. #7471
Added the option to configure the name of the output segmentation layer in the neuron inferral job. #7472
Adhoc mesh rendering is now available for ND datasets.#7394
When setting up WEBKNOSSOS from the git repository for development, the organization directory for storing datasets is now automatically created on startup. #7517
Multiple segments can be dragged and dropped in the segments tab. #7536
Added the option to convert agglomerate skeletons to freely modifiable skeletons in the context menu of the Skeleton tab. #7537
The annotation list in the dashboard now also shows segment counts of volume annotations (after they have been edited). #7548
The buildinfo route now reports the supported HTTP API versions. #7581
After deleting specific teams, projects and task types, their names can now be re-used when creating new ones. #7573

Changed¶

Improved loading speed of the annotation list. #7410
Improved loading speed for the users list. #7466
Admins and Team Managers can now also download job exports for jobs of other users, if they have the link. #7462
Updated some dependencies of the backend code (play 2.9, sbt 1.9, minor upgrades for others) for optimized performance. #7366
Processing jobs can now be distributed to multiple webknossos-workers with finer-grained configurability. Compare migration guide. #7463
A warning is shown when the user tries to annotate volume data in the "Overwrite Empty" mode when no voxels were changed. #7526
Updated antd UI library from version 4.24.8 to 4.24.15. #7505
Changed the default dataset search mode to also search in subfolders. #7539
When clicking a segment in the viewport, it is automatically focused in the segment list. A corresponding context menu entry was added as well. #7512
Updated the isValidName route in the API to return 200 for valid and invalid names. With this, the API version was bumped up to 6. #7550
Upgraded to Play 3. #7562
When no Email Address for New-User Notifications is configured, the organization owner will be notified. For overtime notifications, the project owner and the organization owner will be notified. #7561
The metadata for ND datasets and their annotation has changed: upper bound of additionalAxes is now stored as an exclusive value, called "end" in the NML format. #7547
Added support for the index_location parameter in sharded Zarr 3 datasets. #7553

Fixed¶

Datasets with annotations can now be deleted. The concerning annotations can no longer be viewed but still be downloaded. #7429
Fixed several deprecation warnings for using antd's Tabs.TabPane components. #7469
Fixed problems when requests for loading data failed (could impact volume data consistency and rendering). #7477
The settings page for non-wkw datasets no longer shows a wall of non-applying errors. #7475
Fixed a bug where dataset deletion for ND datasets and datasets with coordinate transforms would not free the name even if no referencing annotations exist. #7495
Fixed a bug where the URL in the sharing link was wrongly decoded before encoding into a URI. #7502
Fixed a bug where loaded meshes were not encoded in the sharing link. #7507
Fixed a bug where meshes (or chunks of them) were always colored white, if they were loaded while the corresponding segmentation layer was disabled. #7507
Fixed a race condition when opening a short link, that would sometimes lead to an error toast. #7507
Fixed that the Segment Statistics feature was not available in the context menu of segment groups and in the context menu of the data viewports. #7510
Fixed rare bug which produced a benign error toast on some mouse interactions. #7525
Fixed a bug where dataset managers were not allowed to assign teams to new datasets that they are only member of. This already worked while editing the dataset later, but not during upload. #7518
Fixed regression in proofreading tool when automatic mesh loading was disabled and a merge/split operation was performed. #7534
Fixed that last dimension value in ND dataset was not loaded. #7535
Fixed the initialization of the mapping list for agglomerate views if json mappings are present. #7537
Fixed a bug where uploading ND volume annotations would lead to errors due to parsing of the chunk paths. #7547
Fixed a bug where listing the annotations of other users would result in empty lists even if there are annotations and you should be allowed to see them. #7563
Fixed the "Download Meshes" functionality which was affected by the recent introduction of the CSP. #7577
Fixed a bug where listing the annotations of other users would result in empty lists even if there are annotations, and you should be allowed to see them. #7563
Fixed errors showing when viewing the annotation list. #7579
Fixed a bug where all-zero chunks/buckets were omitted when downloading volume annotation even in case of a fallback segmentation layer, where their zeroed-bucket information is actually needed. #7576
Fixed a bug where zarr3 datasets with sharding that didn’t specify an explicit index_location in their metadata could not be read. #7583

Removed¶

Removed Swagger/OpenAPI json description of the HTTP API. #7494
Removed several unused frontend libraries. #7521

23.12.0 - 2023-11-27¶

Commits

Highlights¶

Zarr datasets can now be directly uploaded to WEBKNOSSOS. #7397

Added¶

Added support for reading uint24 rgb layers in datasets with zarr2/zarr3/n5/neuroglancerPrecomputed format, as used for voxelytics predictions. #7413
Adding a remote dataset can now be done by providing a Neuroglancer URI. #7416
Added a filter to the Task List->Stats column to quickly filter for tasks with "Prending", "In-Progress" or "Finished" instances. #7430

Changed¶

An appropriate error is returned when requesting an API version that is higher than the current version. #7424
Upgraded FossilDB database used to store annotation data to version 0.1.27. #7440

Fixed¶

Searching the segments in the sidebar will highlight newly focused segments properly now. #7406
Fixed a bug when opening a task for which a mag restriction exists. The bug only occurred when the referenced mag didn't exist in the dataset. #7403
Fixed that trees with ids around 1023 were invisible on some systems. #7443
Fixed styling issues with the maintenance banner so that it no longer overlaps other menus, tabs, and buttons. #7421
Exploring HTTP uris of unknown hosts no longer causes an exception error message to be displayed. #7422
Fixed the initialization of the dark theme if it was active during page load. #7446
Fixed a rare bug in ad-hoc meshing for voxelytics-created segmentations with agglomerate mappings. #7449

23.11.0 - 2023-10-24¶

Commits

Highlights¶

Added a new tool that allows either measuring the distance of a path or a non-self-crossing area. #7258
For setups with webknossos-worker: Added a feature to create an engaging animation video of a dataset and its meshes processed in Blender. #7348

Added¶

Added social media link previews for links to datasets and annotations (only if they are public or if the links contain sharing tokens). #7331
Loading sharded zarr3 datasets is now significantly faster. #7363 and #7370
OME-NGFF datasets with only 2 dimensions can now be imported and viewed. #7349
Higher-dimension coordinates (e.g., for the t axis) are now encoded in the URL, too, so that reloading the page will keep you at your current position. Only relevant for 4D datasets. #7328
WEBKNOSSOS can now also explore datasets on the local file system if enabled in the new config key datastore.localFolderWhitelist. #7389
It is now possible to download volume annotations as zarr- rather than wkw-based zip. This case also supports annotations on timeseries (ND) datasets. #7288

Changed¶

Updated backend code to Scala 2.13, with upgraded Dependencies for optimized performance. #7327
Remote datasets with a datasource-properties.json can now also be imported without the need for OME metadata. #7372
Occurrences of isosurface were renamed to ad-hoc mesh. This also applies to configuration files. #7350
Improved user interface to start automatic AI analysis. #7368

Fixed¶

Fixed that some segment (group) actions were not properly disabled for non-editable segmentation layers. #7207
Fixed a bug where data from zarr2 datasets that have a channel axis was broken. #7374
Fixed a bug which changed the cursor position while editing the name of a tree or the comment of a node. #7390
Streaming sharded zarr3 datasets from servers which do not respond with Accept-Ranges header is now possible. #7392

23.10.2 - 2023-09-26¶

Commits

Fixed¶

Fixed that segment statistics were requested in the wrong resolution and without properly considering the dataset scale. #7355

23.10.1 - 2023-09-22¶

Commits

Fixed¶

Fixed that auto-saving only took place every 5 minutes instead of every 30 seconds. #7352

23.10.0 - 2023-09-21¶

Commits

Highlights¶

Datasets and annotations can now be more than 3-dimensional, using additional coordinates. #7136
Volume and bounding box information is shown in segments' context menus as well as in a separate modal in the segments tab. There is also an option to export the statistics. #7249

Added¶

Added disabled drag handles to volume and skeleton layers for visual consistency. These layer cannot be dragged or reordered. #7295
Dataset thumbnails for grayscale layers can now be colored using the value in the view configuration. #7255
OpenID Connect authorization is now compatible with Providers that send the user information in an id_token. #7294
Segments and segment groups can be modified via the JS API. The following functions are available: registerSegment, removeSegment, updateSegment, createSegmentGroup, renameSegmentGroup, deleteSegmentGroup. #7332
A banner underneath the navigation bar informs about current and upcoming maintenances of WEBKNOSSOS. #7284
The AI-based quick select tool can now also be used for ND datasets. #7287

Changed¶

On datasets with segment indices, ad-hoc meshing can now create non-connected meshes. #7244
Annotating volume data uses a transaction-based mechanism now. As a result, WK is more robust against partial saves (i.e., due to a crashing tab). #7264
Improved speed of saving volume data. #7264
Improved progress indicator when saving volume data. #7264
Adapted Zarr 3 implementations to recent changes in the specification (index codecs, zstd codec). #7305
When importing datasets with additional axes (more than 3 dimensions), the axis names are now sanitized and checked for duplicates. #7308

Fixed¶

Fixed that the deletion of a selected segment would crash the segments tab. #7316
Fixed reading sharded Zarr 3 data from the local file system. #7321
Fixed no-bucket data zipfile when downloading volume annotations. #7323
Fixed too tight assertions when saving annotations, leading to failed save requests. #7326
Fixed a bug when saving large amounts of skeleton annotation data at once. #7329
Fixed a bug that prevented downloading public skeleton-only annotations by other users. #7347

23.09.0 - 2023-08-29¶

Commits

Highlights¶

Added option to select multiple segments in the segment list in order to perform batch actions. #7242
Added the option to change the ordering of color layers via drag and drop. This is useful when using the cover blend mode. #7188

Added¶

Added configuration to require users' emails to be verified, added flow to verify emails via link. #7161
Added a route to explore and add remote datasets via API. #7176
Added a new button to the layer settings in view only dataset mode to save the current view configuration as the dataset's default. #7205
If a dataset layer is transformed (using an affine matrix or a thin plate spline), it can be dynamically shown without that transform via the layers sidebar. All other layers will be transformed accordingly. #7246
OpenID Connect authorization can now use a client secret for added security. #7263

Changed¶

Small messages during annotating (e.g. “finished undo”, “applying mapping…”) are now click-through, so they do not block users from selecting tools. #7239
When exploring remote NGFF datasets with channels, layer names and colors are automatically imported if available in the metadata. #7251
Annotating volume data uses a transaction-based mechanism now. As a result, WK is more robust against partial saves (i.e., due to a crashing tab). #7264
Improved speed of saving volume data. #7264
Improved progress indicator when saving volume data. #7264
The order of color layers can now also be manipulated in additive blend mode (see #7188). #7289
OpenID Connect authorization now fetches the server’s public key automatically. The config keys singleSignOn.openIdConnect.publicKey and singleSignOn.openIdConnect.publicKeyAlgorithm are now unused. 7267
When importing a remote dataset and adding another layer with a different voxel size, that layer is now scaled to match the first layer. #7213

Fixed¶

Fixed that it was possible to have larger active segment ids than supported by the data type of the segmentation layer which caused the segmentation ids to overflow. #7240
Fixed that folders could appear in the dataset search output in the dashboard. #7232
Fixed that the edit icon for an annotation description could disappear in Firefox. #7250
Fixed that assigning an invalid script name (e.g. with special characters) would trigger an error in the database. Now leads to a more descriptive error. #7525
Fixed rendering error when multiple segmentation layers exist and the user switched between these. #7291

Breaking Changes¶

The task and project api have changed. Make sure to update to the latest webknossos python library version when interacting with task and projects via the python library. Compare webknossos-libs#930. #7220

23.08.0 - 2023-07-24¶

Commits

Highlights¶

Added batch actions for segment groups, such as changing the color and loading or downloading all corresponding meshes. #7164.
Improved support for touch devices by adding floating buttons for easier navigation and layout changes. #7178
The brush size can now be changed by selecting brush size presets. These presets are user configurable by assigning the current brush size to any of the preset buttons. Additionally the preset brush sizes can be set with keyboard shortcuts. #7101

Added¶

Added a search feature for segments and segment groups. Listed segments/groups can be searched by id and name. #7175
Added a modal to the voxelytics workflow view that lists all artifacts with their file size and inode count. This helps to identify the largest artifacts to free disk space. #7152
Added new graphics and restyled empty dashboards. #7008
Added warning when using WEBKNOSSOS in an outdated browser. #7165
Re-added optional antialiasing for rendering. #7180
Added support for transformations with thin plate splines. #7131
WEBKNOSSOS can now read S3 remote dataset credentials from environment variables AWS_ACCESS_KEY_ID and AWS_SECRET_KEY. Those will be used, if available, when accessing remote datasets for which no explicit credentials are supplied. #7170
Added security.txt according to RFC 9116. The content is configurable and it can be disabled. #7182
Added routes for super-users to manage users and organizations. #7196
Added tooltips to explain the task actions "Reset" and "Reset and Cancel". #7201
Thumbnail improvements: Thumbnails now use intensity configuration, thumbnails can now be created for float datasets, and they are cached across webknossos restarts. #7190

Changed¶

Redesigned the info tab in the right-hand sidebar to be fit the new branding and design language. #7110
The proofreading tool is always visible now (even when disabled). #7174
Optimized processing of parallel requests (new thread pool configuration, asynchronous FossilDB client), improving performance and reducing idle waiting. #7139
Renamed "open" tasks to "pending" and slightly redesigned the available task assignment view for clarity. #7187
Being the uploader of a dataset no longer grants edit permissions on that dataset. #7200
Enabled the "Shift + middle-click" shortcut to load agglomerate skeletons for all tools, not just the Skeleton tool. #7212

Fixed¶

Fixed rare rendering bug at viewport edge for anisotropic datasets. #7163
Fixed the dataset search which was broken when only the root folder existed. #7177
Correctly use configured fill-value for missing chunks of remote datasets hosted on gcs or s3. #7198
Correctly use configured fill-value for missing chunks of local non-wkw datasets. #7216
Adapted the proofreading docs to reflect the current state of the proofreading tool. #7212
Fixed a bug when adding remote datasets while not having write-access to the root folder. #7221

Removed¶

Removed the "Globalize Floodfill" feature that could extend partial floodfills across an entire dataset. Please use the fill tool multiple times instead or make use of the proofreading tool when correcting large structures. #7173

23.07.0 - 2023-06-20¶

Commits

Highlights¶

Added new shortcuts for fast tool switching. Look at the updated Keyboard Shortcuts documentation to see the new shortcuts. #7112
Creating bounding boxes can now be done by dragging the left mouse button (when the bounding box tool is selected). To move around in the dataset while this tool is active, keep ALT pressed. #7118

Added¶

Subfolders of the currently active folder are now also rendered in the dataset table in the dashboard. #6996
Added ability to view zarr v3 datasets. #7079
Added an index structure for volume annotation segments, in preparation for per-segment statistics. #7063
Instead of showing all possible action items next to each other, there is now an overflow menu for layer actions. #7123

Changed¶

Agglomerate skeletons can only be modified if the proofreading tool is active so they stay in sync with the underlying segmentation and agglomerate graph. Agglomerate skeletons cannot be modified using any other means. They are marked in the skeleton list using the clipboard icon of the proofreading tool. When exporting skeletons in the NML format, trees ("things") now have a type property which is either "DEFAULT" or "AGGLOMERATE". #7086
The cache for remote dataset array contents can now have a configured size in bytes. New config option datastore.cache.imageArrayChunks.maxSizeBytes. Default is 2 GB, consider increasing for production. #7067
Optimized processing of parallel requests for remote datasets, improving performance and reducing idle waiting. #7137

Fixed¶

Fixed a bug where some volume annotations could not be downloaded. #7115
Fixed reading of some remote datasets where invalid data would follow valid gzip data, causing the decompression to fail. #7119
Fixed problems which could arise when annotating volume data at negative positions (which is not supported and is properly ignored now). #7124
Fixed some requests failing for streaming remote data via HTTP, which was observed when streaming data via Zarr from another WEBKNOSSOS instance. #7125
Fixed that the brush preview was inaccurate in some scenarios. #7129
Fixed order of decompression on neuroglancer precomputed datasets, which caused some segmentation layers to not load correctly. #7135

Removed¶

Support for webknososs-connect data store servers has been removed. Use the "Add Remote Dataset" functionality instead. #7031

23.06.0 - 2023-05-30¶

Commits

Highlights¶

Added a machine-learning based quick select mode. Activate it via the "AI" button in the toolbar after selecting the quick-select tool. #7051
Added segment groups so that segments can be organized in a hierarchy (similar to skeletons). #6966
Added a new "cover" blend mode which renders the visible layers on top of each other. The new blend mode can be selected in the Data Rendering settings in the settings tab of the left side bar. #6936

Added¶

In addition to drag and drop, the selected tree(s) in the Skeleton tab can also be moved into another group by right-clicking the target group and selecting "Move selected tree(s) here". #7005
Added support for remote datasets encoded with brotli. #7041
Teams can be edited more straight-forwardly in a popup in the team edit page. #7043
Added support to download layers of a dataset as (OME) TIFF files in the download modal when viewing a dataset. #7068
Annotations with Editable Mappings (a.k.a Supervoxel Proofreading) can now be merged. #7026
The file size and inodes of artifacts are now aggregated and shown in the Voxelytics workflow list. #7071
It is possible to disable the automatic loading of meshes during proofreading. ##7076
When viewing a public dataset by another organization, the organization is shown next to the dataset list, and when viewing the dataset or an annotation. #7087

Changed¶

Loading of precomputed meshes got significantly faster (especially when using a mesh file for an oversegmentation with an applied agglomerate mapping). #7001
Improved speed of proofreading by only reloading affected areas after a split or merge. #7050
The minimum length of layer names in datasets was set from 3 to 1, enabling single-character names for layers. #7064
All dataset managers are now allowed to see all voxelytics workflow reports created in their organization. Previously, only admins could see all workflow reports, with other users seeing only their own. #7080
Improved performance for large meshes, especially when loaded from a precomputed oversegmentation mesh file. #7077
Slight increased the spacing and width of some VX reports elements. #7094

Fixed¶

Fixed that changing a segment color could lead to a crash. #7000
The fill_value property of zarr dataset is now used when it is not a number. #7017
Fixed a bug that made downloads of public annotations fail occasionally. #7025
Fixed layouting of used storage space on the organization page. #7034
Fixed a bug where updating skeleton annotation tree group visibility would break the annotation. #7037
Fixed importing Neuroglancer Precomputed datasets that have a voxel offset in their header. #7019, #7062
Fixed reading Neuroglancer Precomputed datasets with non-integer resolutions. #7041
Fixed a bug where invalid email addresses were not readable in dark mode on the login/signup pages. #7052
Fixed a bug where users could sometimes not access their own time tracking information. #7055
Fixed a bug in the wallTime calculation of the Voxelytics reports. #7059
Fixed a bug where thumbnails and raw data requests with non-bucket-aligned positions would show data at slightly wrong positions. #7058
Avoid crashes when exporting big STL files. #7074
Fixed rare rendering bug for datasets with multiple layers and differing magnifications. #7066
Fixed a bug where duplicating annotations with Editable Mappings could lead to a server-side endless loop. #7026
Fixed the datasource-properties.json route for zarr-streaminge export of datasets that are not wkw/zarr. #7065
Fixed an issue where you could no longer invite users to your organization even though you had space left. #7078
Fixed displayed units of used storage in the organization's overview page. #7057
Fixed a rendering bug that could occur when a dataset layer has missing mags (e.g., the first mag is 8-8-8). #7082
Fixed a bug where some volume annotations could not be duplicated or used as tasks. #7085
Fixed a superfluous rectangular geometry rendered at 0,0,0. #7088

23.05.2 - 2023-05-08¶

Commits

Fixed¶

Fixed a bug where users could sometimes not access their own time tracking information. #7055

23.05.1 - 2023-05-02¶

Commits

Fixed¶

Fixed rendering issues on some affected systems that led to "black holes". #7018
Added a workaround for a WebGL crash which could appear when a dataset contained many segmentation layers. #6995

23.05.0 - 2023-04-25¶

Commits

Highlights¶

Segments can now be removed from the segment list via the context menu. #6944
Added support for viewing neuroglancer precomputed segmentations using "compressed segmentation" compression. #6947

Added¶

WEBKNOSSOS screenshots now include a logo in the lower left corner. Users with a paid license can disable this feature in the viewport options in the settings tab on the left side of the screen. #6910
Added support for datasets with mixed magnifications (e.g., one layer contains mag 2-2-2 and another contains 2-2-1). #6943
Added rendering precomputed meshes with level of detail depending on the zoom of the 3D viewport. This feature only works with version 3 mesh files. #6909
Editing the meta data of segments (e.g., the name) is now undoable. #6944
Added more icons and small redesigns for various pages in line with the new branding. #6938
Added more graphics and branding to job notification emails. #6994
Added action button in Team Admin page that links to the User Admin page to edit team members there. #6958

Changed¶

Moved the view mode selection in the toolbar next to the position field. #6949
Redesigned welcome toast for new, anonymous users with new branding. #6961
When saving annotations, the URL of the webknossos instance is stored in the resulting NML file. #6964

Fixed¶

Fixed unintended dependencies between segments of different volume layers which used the same segment id. Now, using the same segment id for segments in different volume layers should work without any problems. #6960
Fixed incorrect initial tab when clicking "Show Annotations" for a user in the user list. Also, the datasets tab was removed from that page as it was the same as the datasets table from the main dashboard. #6957
Fixed that unsaved changes were shown when opening an annotation, although there weren't any. #6972
Fixed misleading email about successful dataset upload, which was in some cases sent even for unusable datasets. #6977
Fixed upload of skeleton annotations with no trees, only bounding boxes, being incorrectly rejected. #6985
Fixed that Google Cloud Storage URLs with bucket names containing underscores could not be parsed. #6998
Fixed regression that caused public datasets to crash when not being logged in. #7010

23.04.2 - 2023-04-14¶

Commits

Fixed¶

Fixed rendering problems in orthogonal when working with nodes that were created in flight or oblique mode. #6978

23.04.1 - 2023-04-06¶

Commits

Fixed¶

Fixed incorrect initial tab when clicking "Show Annotations" for a user in the user list. Also, the datasets tab was removed from that page as it was the same as the datasets table from the main dashboard. #6957

23.04.0 - 2023-03-27¶

Commits

Highlights¶

Added email notifications for WK worker jobs. #6918
Added support for viewing sharded neuroglancer precomputed datasets. #6920

Added¶

Added support for datasets where layers are transformed individually (with an affine matrix). Transformations can be specified via datasource-properties.json or via JS API (will be ephemeral, then). #6748
Added list of all respective team members to the administration page for teams. #6915
Added support for uploading zip64 files. #6939

Changed¶

Interpolation during rendering is now more performance intensive, since the rendering approach was changed. Therefore, interpolation is disabled by default. On the flip side, the rendered quality is often higher than it used to be. #6748
Updated the styling of the "welcome" screen for new users to be in line with the new branding. #6904
Improved Terms-of-Service modal (e.g., allow to switch organization even when modal was blocking the remaining usage of WEBKNOSSOS). #6930
Uploads are now blocked when the organization’s storage quota is exceeded. #6893

Fixed¶

Fixed an issue with text hints not being visible on the logout page for dark mode users. #6916
Fixed creating task types with a selected preferred mode. #6928
Fixed support for rendering of negative floats. #6895
Fixed caching issues with webworkers. #6932
Fixed download button for annotations which was disabled in some cases. #6931
Fixed antd deprecation warning for Dropdown menus. #6898

23.03.1 - 2023-03-14¶

Commits

Added¶

Added support for remote Zarr datasets with a datasource-properties.json as created by the WEBKNOSSOS Python library. #6879

Changed¶

Upgraded antd UI library to v4.24.8 #6865
The view mode dropdown was slimmed down by using icons to make the toolbar more space efficient. #6900

Fixed¶

Fixed a bug where N5 datasets reading with end-chunks that have a chunk size differing from the metadata-supplied chunk size would fail for some areas. #6890
Fixed potential crash when trying to edit certain annotation properties of a shared annotation. #6892
Fixed a bug where merging multiple volume annotations would result in inconsistent segment lists. #6882
Fixed a bug where uploading multiple annotations with volume layers at once would fail. #6882
Fixed a bug where dates were formatted incorrectly in Voxelytics reports. #6908
Fixed a rare bug which could cause an incorrectly initialized annotation so that changes were not saved in the current session. #6914

23.03.0 - 2023-02-28¶

Commits

Highlights¶

Remote datasets can now also be streamed from Google Cloud Storage URIs (gs://). #6775
Remote volume datasets in the neuroglancer precomputed format can now be viewed in WEBKNOSSOS. #6716
Added new mesh-related menu items to the context menu when a mesh is hovered in the 3d viewport. #6813

Added¶

If an annotation that others are allowed to edit is opened, it will now be automatically locked. This prevents conflicts when multiple users try to edit it at the same time. #6819
Highlight 'organization owner' in Admin>User page. #6832
Added OME-TIFF export for bounding boxes. #6838 #6874
Added functions to get and set segment colors to the frontend API (api.data.{getSegmentColor,setSegmentColor}). #6853

Changed¶

Limit paid team sharing features to respective organization plans. #6767
Rewrite the database tools in tools/postgres to JavaScript and adding support for non-default Postgres username-password combinations. #6803
Added owner name to organization page. #6811
Remove multiline support from <inputcomponent>. <a href="https://github.com/scalableminds/webknossos/pull/6839">#6839</a></inputcomponent>
Improved the performance of the dataset table in the dashboard. #6834
Updated the styling and background of login, password reset/change and sign up pages. #6844
Replaced date handling and formatting library momentjs with dayjs. #6849

Fixed¶

Fixed saving allowed teams in dataset settings. #6817
Fixed log streaming in Voxelytics workflow reports. #6828 #6831
Fixed some layouting issues with line breaks in segment list/dataset info tab. #6799
Fixed basic auth for exploring remote http datasets. #6866
Fixed the layouting in the connectome tab. #6864
Fixed that the quick-select and floodfill tool didn't update the segment list. #6867
Fixed deprecation warnings for antd' component in Navbar. #6860
Fixed that trying to reload a precomputed mesh via context menu could crash webKnossos. #6875

Removed¶

Removed the old Datasets tab in favor of the Dataset Folders tab. #6834

23.02.1 - 2023-02-07¶

Commits

Fixed¶

Fixed a benign error message which briefly appeared after logging in. #6810

23.02.0 - 2023-02-01¶

Commits

Highlights¶

Changed branding of WEBKNOSSOS including a new logo, new primary colors, and UPPERCASE name. #6739
Precomputed meshes can now be loaded even when a mapping is active (HDF5 or an editable mapping produced by the proofreading tool). The precomputed mesh has to be computed without a mapping for this to work. #6569

Added¶

The target folder of a dataset can now be specified during upload. Also, clicking "Add Dataset" from an active folder will upload the dataset to that folder by default. #6704
The storage used by an organization’s datasets can now be measured. #6685

Changed¶

For remote datasets that require authentication, credentials are no longer stored in the respective JSON. #6646
Improved performance of opening a dataset or annotation. #6711
Redesigned organization page to include more infos on organization users, storage, webKnossos plan and provided opportunities to upgrade. #6602
Improves performance for ingesting Voxelytics reporting data. #6732
Implements statistics from combined workflow runs in the Voxelytics reporting. #6732
Limit paid task/project management features to respective organization plans. 6767
The dataset list route GET api/datasets no longer respects the isEditable filter. #6759
Upgrade linter to Rome v11.0.0. #6785

Fixed¶

Fixed node selection and context menu for node ids greater than 130813. #6724 and #6731
Fixed the validation of some neuroglancer URLs during import. #6722
Fixed a bug where deleting a dataset would fail if its representation on disk was already missing. #6720
Fixed a bug where a user with multiple organizations could not log in anymore after one of their organization accounts got deactivated. #6719
Fixed rare crash in new Datasets tab in dashboard. #6750 and #6753
Fixed toggling "Render missing data black" when being logged out. #6772
Fixed incorrect loading of precomputed meshes from mesh files that were computed for a specific mapping. #6771
Fixed a bug where remote datasets without authentication could not be explored. #6764
Fixed deprecation warnings for antd props. #6765
Fixed a bug where direct task assignment to a single user would fail. #6777
Fixed a bug where the dataset folders view would not list public datasets if the requesting user could not also access the dataset for other reasons, like being admin. #6759
Fixed a bug where zarr-streamed datasets would produce (very rare) rendering errors. #6782
Fixed a bug where publicly shared annotations were not viewable by users without an account. #6784
Fixed proofreading when mag 1 doesn't exist for segmentation layer #6795
Fixed that the proofreading tool allowed to split/merge with segment 0 which led to an inconsistent state. #6793

Breaking Changes¶

Changes the storage backend for Voxelytics logging from Elasticsearch to Loki. #6770
The dataset list route GET api/datasets no longer respects the isEditable filter. #6759

23.01.0 - 2023-01-03¶

Commits

Highlights¶

Added a new datasets tab to the dashboard which supports managing datasets in folders. Folders can be organized hierarchically and datasets can be moved into these folders. Selecting a dataset will show dataset details in a sidebar. #6591
webKnossos is now able to recover from a lost webGL context. #6663
Major performance improvements for brushing in coarse magnifications. #6708

Added¶

Added sign in via OIDC. #6534
Added the option to search a specific folder in the new datasets tab. #6677
The new datasets tab in the dashboard allows multi-selection of datasets so that multiple datasets can be moved to a folder at once. As in typical file explorers, CTRL + left click adds individual datasets to the current selection. Shift + left click selects a range of datasets. #6683

Changed¶

Bulk task creation now needs the taskTypeId, the task type summary will no longer be accepted. #6640
Error handling and reporting is more robust now. #6700
The Quick-Select settings are opened (and closed) automatically when labeling with the preview mode. That way, bulk labelings with preview mode don't require constantly opening the settings manually. #6706

Fixed¶

Fixed import of N5 datasets. #6668
Fixed a bug where it was possible to create invalid an state by deleting teams that are referenced elsewhere. 6664
Miscellaneous fixes for the new folder UI. #6674
Fixed import of remote datasets with multiple layers and differing resolution pyramid. #6670
Fixed broken Get-new-Task button in task dashboard. #6677
Fixed access of remote datasets using the Amazon S3 protocol #6679
Fixed a bug in line measurement that would lead to an infinite loop. #6689
Fixed a bug where malformed json files could lead to uncaught exceptions.#6691
Fixed rare crash in publications page. #6700
Respect the config value mail.smtp.auth (used to be ignored, always using true) #6692

Removed¶

Breaking Changes¶

22.12.0 - 2022-11-24¶

Commits

Highlights¶

Added a new Quick-Select tool for volume annotation. This tools allows to draw a rectangle over a segment to annotate it automatically. The tool operates on the intensity data of the visible color layer and automatically fills out the segment starting from the center of the rectangle. Next to the tool, there is a settings button which allows to enable a preview mode and to tweak some other parameters. If the preview is enabled, the parameters can be fine-tuned while the preview updates instantly. #6542
The scale bar is now included in screenshots of the viewports made using the Q shortcut or the "Screenshot" menu entry. If the scale bar should not be included, disable it using "Settings - Viewport Options - Show Scalebars". #6644

Added¶

The largest segment id for a segmentation layer can be computed automatically from the dataset settings page. #6415
Button for switching organizations for Voxelytics workflows. #6572
Added ability to shuffle / set colors for a whole tree group. #6586
Annotation layers can now be removed. #6593
When adding remote Zarr datasets with multiple channels, channels are converted into layers. #6609
When adding a remote OME-NGFF dataset with labels, these are added as segmentation layers. #6638
When creating an annotation from the dataset view, a previously selected mapping of the segmentation layer is now automatically selected in the volume annotation layer fallback segmentation as well. #6647

Changed¶

The log viewer in the Voxelytics workflow reporting now uses a virtualized list. #6579
Node positions are always handled as integers. They have always been persisted as integers by the server, anyway, but the session in which a node was created handled the position as floating point in earlier versions. #6589
Jobs can no longer be started on datastores without workers. #6595
When downloading volume annotations with volume data skipped, the nml volume tag is now included anyway (but has no location attribute in this case). #6566
Re-phrased some backend (error) messages to improve clarity and provide helping hints. #6616
The layer visibility is now encoded in the sharing link. The user opening the link will see the same layers that were visible when copying the link. #6634
Voxelytics workflows can now be viewed by anyone with the link who is in the right organization. #6622
Improve performance for handling of volume annotation data (saving/undo/redo). #6652
When importing an annotation into an existing annotation, webKnossos ensures that bounding boxes are not duplicated in case they exist in the current and imported annotation. #6648
Reworked the proofreading mode so that agglomerate skeletons are no longer needed (nor automatically loaded). Instead, segments can be selected by left-clicking onto them, indicated by a small white cross. To merge or split agglomerates, then either use the shortcuts Shift + Leftclick/Ctrl + Leftclick or use the context menu. #6625

Fixed¶

Fixed a bug in the dataset import view, where the layer name text field would lose focus after each key press. #6615
Fixed importing NGFF Zarr datasets with non-scale transforms. #6621
Fixed a regression in NGFF Zarr import for datasets with no channel axis. #6636
Fixed broken creation of tasks using base NMLs. #6634
Fixed that the precomputation of meshes didn't take the active mapping into account. #6651
Fixed false-positive warning about an outdated annotation version. #6656
Fixed that segment statistics seemed to be available but broken for segments without index. #7377

22.11.2 - 2022-11-10¶

Commits

Changed¶

When merging annotations, bounding boxes are no longer duplicated. #6576

Fixed¶

Fixed importing a dataset from disk. #6615

22.11.1 - 2022-10-27¶

Commits

Added¶

Turned successful dataset conversions into a clickable link. #6583

Fixed¶

Fixed a rare crash in newer Firefox versions. #6561
Fixed the positions of precomputed meshes when using a v3 mesh file. #6588

22.11.0 - 2022-10-24¶

Commits

Highlights¶

Remote n5 datasets can now also be explored and added. #6520
Tasks can now be assigned to individual users directly. #6551
Support for a new mesh file format which allows up to billions of meshes. #6491

Added¶

The task creation page now links to creation pages for task types, projects etc., for a smoother task administration experience. #6513
Improved performance for applying agglomerate mappings on segmentation data. #6532
Added backspace as an additional keyboard shortcut for deleting the active node. #6554
When reloading a layer, because the underlying data has changed, the histogram will also be reloaded and reflect the changes. #6537
Enable "What's New" update information for all instances. #6563
Add context-menu option to delete skeleton root group. #6553
Added remaining task time estimation (ETA) for Voxelytics tasks in workflow reporting. #6564
Added a help button to the UI to send questions and feedbacks to the dev team. #6560

Changed¶

Creating tasks in bulk now also supports referencing task types by their summary instead of id. #6486
Navbar changes: Move dropdown menu into separate Menu button. Removed toggle-button (cog icon)for left-hand side bar from navbar. #6558
Upgraded Typescript to v4.8 #6567

Fixed¶

Fixed a bug where some file requests replied with error 400 instead of 404, confusing some zarr clients. #6515
Fixed URL for private Zarr streaming links to volume annotations. #6515
Fixed a bug where the transform of a new mesh file wasn't taken into account for the rendering of meshes. #6552
Fixed a rare crash when splitting/merging a large skeleton. #6557
Fixed a bug where some features were unavailable for annotations for datasets of foreign organizations. #6548

22.10.0 - 2022-09-27¶

Commits

Highlights¶

Added a context menu option to extract the shortest path between two nodes as a new tree. Select the source node and open the context menu by right-clicking on another node in the same tree. #6423
Add setting for gamma correction for color and grayscale layers in the left sidebar. #6439
Added a context menu option to separate an agglomerate skeleton using Min-Cut. Activate the Proofreading tool, select the source node and open the context menu by right-clicking on the target node which you would like to separate through Min-Cut. #6361
The color of a segments can now be changed in the segments tab. Rightclick a segment in the list and select "Change Color" to open a color picker. #6372
Sharing links are shortened by default. Within the sharing modal, this shortening behavior can be disabled. #6461
The largestSegmentId is no longer a required property for segmentation layers. It is still recommended to set the property, since the generation of new segment IDs is blocked during volume annotation. However, annotating with manually set IDs is still possible. This change simplifies the import of datasets into webKnossos. #6414

Added¶

Zarr-based remote dataset import now also works for public AWS S3 endpoints with no credentials. #6421
Added a "clear" button to reset skeletons/meshes after successful mergers/split. #6459
The proofreading tool now supports merging and splitting (via min-cut) agglomerates by right-clicking a segment (and not a node). Note that there still has to be an active node so that both partners of the operation are defined. #6464
Added workflow reporting and logging features for Voxelytics into webKnossos. If activated, the workflows can be accessed from the Administration > Voxelytics menu item. #6416 #6460
Added possibility to read N5 datasets. #6466
Added "shift + w" shortcut to cycle backwards through annotation tools. #6493

Changed¶

Selecting a node with the proofreading tool won't have any side effects anymore. Previous versions could load additional agglomerate skeletons in certain scenarios which could be confusing. #6477
Removed optional "resolution" parameter from /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data route. Use mag instead. #6479
Changed how volumes containing no data are stored. Now the selection of magnifications is correctly exported and imported. #6481
The "Restore Older Version" list is now paginated which improves performance for in case many versions exist. #6483

Fixed¶

Fixed sharing button for users who are currently visiting a dataset or annotation which was shared with them. #6438
Fixed the duplicate function for annotations with an editable mapping (a.k.a. supervoxel proofreading) layer. #6446
Fixed isosurface loading for volume annotations with mappings. #6458
Fixed importing of remote datastore (e.g., zarr) when datastore is set up separately. #6462
Fixed a crash which could happen when using the "Automatically clip histogram" feature in certain scenarios. #6433
Fixed loading agglomerate skeletons for agglomerate ids larger than 2^31. #6472
Fixed bug which could lead to conflict-warnings even though there weren't any. #6477
Fixed that one could not change the color of a segment or tree in Firefox. #6488
Fixed validation of layer selection when trying to start globalization of floodfills. #6497
Fixed filtering for public datasets in dataset table. #6496

22.09.0 - 2022-08-25¶

Commits

Highlights¶

Added an "extrude segment" feature which is similar to the old "copy from previous slice" feature. The segment interpolation and the new segment extrusion feature are both available via the toolbar (see the dropdown icon which was added to the old interpolation button). #6370
The owner of an annotation can allow other users, who may see the annotation, to also edit it. Note that parallel writes are not supported and would lead to conflicts. #6236
Added support for ad-hoc meshing for volume annotation layers with fallback segmentations. #6369
Added support for 64-bit segmentations (uint64). Note that the actual support only covers IDs up to 2^53 - 1 (matches the JavaScript number type). Also note that JSON mappings are only compatible with segment ids that only use the lower 32 bits. #6317
WebKnossos now remembers the tool that was active in between disabling and enabling the segmentation layer. #6362
The Add Dataset view now hosts an Add Zarr Dataset tab to explore, configure and import remote Zarr datasets. #6335
Added a UI to manage Zarr links for an annotation so that the annotation can be streamed to third-party tools. This change also includes new backend API routes for using the (private) zarr links to annotations as well as creating them. #6367

Added¶

Segmentation layers which were not previously editable now show an (un)lock icon button which shortcuts to the Add Volume Layer modal with the layer being preselected. #6330
The NML file in volume annotation download now includes segment metadata like names and anchor positions. #6347
Added new backend API route for requesting all publications. Those publications can now have also attached annotations. #6315
Added a "duplicate" button for annotations. #6386
Added new filter options for the dataset list api at api/datasets: organizationName: String, onlyMyOrganization: Boolean, uploaderId: String #6377

Changed¶

webKnossos uses WebGL 2 instead of WebGL 1 now. In case your browser/hardware does not support this, webKnossos will alert you and you need to upgrade your system. #6350
The sharing modal now automatically saves changes of the sharing options. #6314
The Layers tab now displays an Add Skeleton Annotation Layer button with which volume-only annotations can be converted to hybrid annotations. #6330
The Zarr directory listings no longer include the current directory “.”. 6359
The default name for volume annotation layers with fallback segmentations is now set to the name of their fallback segmentation layer, no longer “Volume”. #6373
The “reload data” button for dataset and annotation layers is now only shown to users who have administrative permissions for the dataset (because the button clears server caches and file handles). #6380
Requests for missing chunks in zarr datasets now return status code 404 instead of 200 with an empty response. #6381
Dataset layer thumbnails now by default show the center of the intersection of all layer bounding boxes, so all layer thumbnails show the same region. 6411

Fixed¶

Fixed a regression where the mapping activation confirmation dialog was never shown. #6346
Fixed an error if multiple proofreading actions were performed in rapid succession. If webKnossos is busy, inputs to the viewports are disabled from now on. #6325
Fixed that ad-hoc meshing would terminate early for large segments. #6352
Fixed a bug where the largestSegmentId of zarr segmentation layers was not propagated from the datasource-properties.json, which broke annotating based on these layers. #6363
Fixed a bug where uploads of wkw datasets with numerical-only layer names would fail. #6382
Public datasets of other organizations are no longer listed during task creation. #6377
Tightened organization isolation security for dataset uploads. #6378
Fixed a bug with undo/redo and volume interpolation/extrusion. #6403
Fixed a regression which caused that uint16 and uint8 segmentations could not be rendered. #6406
Fixed a bug which prevented keyboard shortcuts from taking affect after expanding/collapsing the sidebar panels using the button icons.#6410
Fixed a bug with the clip histogram button to prevent it from showing a loading spinner forever in some cases. #6407
Fixed an issue whereby a warning toast would be triggered every time the 3D viewport is put into fullscreen mode. #6412

Removed¶

The Annotation Type label was removed from the info tab. #6330
Removed the possibility to load data from foreign webKnossos datastores. Use Zarr streaming instead. #6392

22.08.0 - 2022-07-20¶

Commits

Highlights¶

Merged the "Shared Annotations" tab into the "Annotations" tab in the user's dashboard. If annotations are shared with you, you can see them in your dashboard. The table can be filtered by owner if you prefer to see only your own annotations. #6230
Add new backend API routes for working with annotations without having to provide a 'type' argument. Note that these support stored annotations (Task and Explorational), but do not work for CompoundTask/CompoundProject/CompoundTaskType annotations. For the latter, please use the original route variants with explicit type. #6285

Added¶

Added a warning for invalid volume layer names. The layer names must now be unique among all layers in an annotation and must not contain url encoded special characters. #6289
Added optional mappingName parameter to requestRawCuboid datastore route, which allows to directly apply a specified mapping in the backend. #6311
Added option to use X-Auth-Token header instead of query parameter in every datastore and tracingstore route. #6312

Changed¶

Changed the name of the volume annotation layer in tasks to be "Volume" instead of "Volume Layer". #6321
Dataset managers are now allowed to change dataset team permissions for all teams they are a member of. #6336

Fixed¶

Fixed that zooming out for datasets with very large scale was not possible until the coarsest level. #6304

22.07.0 - 2022-06-28¶

Commits

Highlights¶

Added a image data download speed indicator to the statusbar. On hover a tooltip is shown that show the total amount of downloaded shard data. #6269
Provide a UI to download/export a dataset in view-mode. The UI explains how to access the data with the python library. #6283

Added¶

Added a warning for when the resolution in the XY viewport on z=1-downsampled datasets becomes too low, explaining the problem and how to mitigate it. #6255
Added the possibility to view and download older versions of read-only annotations. #6274
Added a proofreading tool which can be used to edit agglomerate mappings. After activating an agglomerate mapping the proofreading tool can be selected. While the tool is active, agglomerates can be clicked to load their agglomerate skeletons. Use the context menu to delete or create edges for those agglomerate skeletons to split or merge agglomerates. The changes will immediately reflect in the segmentation and meshes. #6195

Changed¶

For the api routes that return annotation info objects, the user field was renamed to owner. User still exists as an alias, but will be removed in a future release. #6250
Slimmed the URLs for annotations by removing Explorational and Task. The old URLs are still supported, but will be redirected to the new format. #6208
When creating a task from a base annotation, the starting position/rotation and bounding box as specified during task creation are now used and overwrite the ones from the original base annotation. #6249
Increased maximum interpolation depth from 8 to 100. #6292

Fixed¶

Fixed that bounding boxes were deletable in read-only tracings although the delete button was disabled. #6273
Fixed that (old) sharing links with tokens did not work, because the token was removed during a redirection. #6281

22.06.1 - 2022-06-16¶

Commits

Fixed¶

Fixed that the context menu broke webKnossos when opening it in dataset-view-mode while no segmentation layer was visible. #6259
Fixed benign error toast when viewing a public annotation without being logged in. #6271

22.06.0 - 2022-05-27¶

Commits

Highlights¶

Added a volume interpolation feature. When triggering the interpolation, the current segment id is interpolated between the current slice and the slice which was annotated last. Note that the feature is forbidden for tasks by default, but can be enabled/recommended. The feature can be used via a button in the toolbar or via the shortcut V. #6162 and #6235
Removed the feature to copy a segment from the previous/next slice with the V shortcut. Use the new volume interpolation feature instead (also bound to V and available via the toolbar). #6235
Selecting "Download" from the annotation actions now opens a new modal, which lets the user select data for download, start TIFF export jobs or copy code snippets to get started quickly with the webKonossos Python Client. #6171
Added a long-running job that materializes annotations as datasets. It merges volume annotations with their base segmentation layer and it applies “merger mode” annotations, allowing to agglomerate segments. Access this feature from the layers sidebar. When merger mode is active, an additional button is shown in the tool bar. #6086

Added¶

Added a batching mechanism to the task creation via NML to support uploading more than 100 NMLs at a time. #6216
Added support to stream zarr files using the corresponding zarr spec. #6144
Added support to stream volume annotations as a zarr data set. #6203
Added segmentation layers to the functionality catching the case that more layers are active that the hardware allows. This prevents rendering issue with more than one segmentation layer and multiple color layers. #6211
Adding a New Volume Layer via the left border tab now gives the option to restrict resolutions for the new layer. #6229
Added Route to get OME-NGFF Headers for a data layer (.zattrs file) following the corresponding spec. #6226
Added Route to get OME-NGFF Headers for Volume annotation. #6242

Changed¶

When creating a new annotation with a volume layer (without fallback) for a dataset which has an existing segmentation layer, the original segmentation layer is still listed (and viewable) in the left sidebar. Earlier versions simply hid the original segmentation layer. #6186
Changing the visibility of a layer within an annotation does not change the visibility of the layer when viewing the corresponding dataset. #6186
While viewing tracings in read-only mode, the options to manipulate the tracing are now disabled. This leads to less confusion as previously the input was silently discarded. #6140.
Changed default of dynamicSpaceDirection property to false to avoid confusion. #6162
Changed the internal protocol for requesting image data. The zoomStep parameter has been replaced by mag. This increases the datastore API version to 2.0 #6159
In annotation list in dashboard, replaced the non-standard word “Trace” by “Open”. #6191
Tiff export via webknossos-worker is now allowed for all datasets that a (logged-in) user can see, no longer only for datasets of their own organization. #6219

Fixed¶

Fixed a bug in the task creation, where creation for some tasks with initial volume data would fail. #6178
Fixed a rendering bug which could cause an incorrect magnification to be rendered in rare scenarios. #6029
Fixed a bug which could cause a segmentation layer's "ID mapping" dropdown to disappear. #6215
Fixed the 3d viewport for datasets with low voxel resolution by making the camera far clipping adaptive to the dataset extent. #6221.
Fixed a non-critical error message when resizing the browser window while webKnossos loaded a dataset or annotation. #6247

22.05.1 - 2022-04-29¶

Commits

Fixed¶

Fixed applying recommended settings when starting a task which provides recommended settings. #6175

Removed¶

Removed the option to download sample-datasets. To explore webKnossos, use the public sample datasets on webknossos.org. #6151

Breaking Changes¶

22.05.0 - 2022-04-26¶

Commits

Highlights¶

The mouse cursor now changes appearance to indicate the currently selected annotation tool #6132

Changed¶

Various changes to the Dataset table in the dashboard #6131:
Renamed "Allowed Teams" column to "Access Permissions".
Add filter functionality to "Access Permissions" column to filter for public datasets.
Removed isActive and isPublic columns to save screen space.
Changed data layer entries to display layer names instead of categories, e.g. "color" --> "axons".
Moved the list of "user with access to the selected dataset" from the dashboard to the respective dataset's settings (Sharing Tab). #6166
Sped up initial requests for remote zarr dataset by using asynchronous caching. #6165

Fixed¶

Fixed a bug that led to an error when drag-'n'-dropping an empty volume annotation in the dataset view. #6116
Fixed rare callstack overflow when annotating large areas. #6076
Fixed the "Copy Slice" shortcut (v and shift + v) in resolutions other than the most detailed one. #6130
Fixed a bug where dataset tags with spaces would be automatically wrapped in quotes. #6159
Fixed a bug where during dataset upload, un-sorted anisotropic mags in the datasource-properties.json could lead to errors. #6167

Removed¶

Removed the functionality to unlink the fallback layer from an existing segmentation layer. Either create an annotation without fallback layer or from within an annotation with a fallback layer, create a new volume layer, instead. #6146

Breaking Changes¶

22.04.0 - 2022-03-22¶

Commits

Highlights¶

The visible meshes are now included in the link copied from the "Share" modal or the "Share" button next to the dataset position. They are automatically loaded for users that open the shared link. #5993
Added a new "Connectome Tab" which can be used to explore connectomes by visualizing neurites and their synaptic connections. Connectome files need to be placed in a connectomes folder inside of the respective segmentation layer. It is possible to craft links that automatically load specific agglomerates and their synapses when opened. For more information refer to https://docs.webknossos.org/webknossos/sharing/annotation_sharing.html#sharing-link-format. #5894

Added¶

Added a context-menu option when right-clicking on skeleton trees to hide/show all other trees but the selected one. Great for inspecting a single tree in isolation. Identical to keyboard shortcut "2". #6102
Added support for reading Zarr image data. #6019

Changed¶

The maximum brush size now depends on the available magnifications. Consequently, one can use a larger brush size when the magnifications of a volume layer are restricted. #6066
Improved stability and speed of volume annotations when annotating large areas. #6055
In dataset upload, linking layers of existing datasets is no longer restricted to public datasets. #6097
Deactivating users with currently active tasks is no longer allowed. #6099

Fixed¶

Fixed a bug that led to crashing the layer settings once the icon for the downsample modal was clicked. #6058
Fixed a bug where toggling between not archived and archived annotations in the "My Annotation" of the dashboard led to inconsistent states and duplicates of annotations. #6058
Fixed a bug where deactivated users would still be listed as allowed to access the datasets of their team. #6070
Fixed occasionally "disappearing" data. #6055
Fixed a bug where remote-origin headers were omitted in error case. #6098
Increased the timeouts for some internal operations like downsampling volume annotations. #6103
Fixed a bug where there was a suggested change in the datasource-config.json was shown for resolution 1 instead of [1,1,1] or vice-versa. #6104

Removed¶

The previously disabled Import Skeleton Button has been removed. The functionality is available via the context menu for datasets with active ID mappings. #6073
Removes experimental (and hidden) automatic brushing feature. Consequently, the corresponding feature flag autoBrushReadyDatasets is not used, anymore. #6107

Breaking Changes¶

22.03.0 - 2022-02-21¶

Commits

Highlights¶

Added experimental min-cut feature to split a segment in a volume annotation with two seeds. #5885
Added a button next to the histogram which adapts the contrast and brightness to the currently visible data. #5961
Viewport scale bars are now dynamically adjusted to display sensible values. #5418

Added¶

Added the option to make a segment's ID active via the right-click context menu in the segments list. #5935
Running uploads can now be cancelled. #5958
Annotations with multiple volume layers can now be uploaded. (Note that merging multiple annotations with multiple volume layers each is not supported.) #6028
Decrease volume annotation download latency by using a different compression level. #6036

Changed¶

Upgraded webpack build tool to v5 and all other webpack related dependencies to their latest version. Enabled persistent caching which speeds up server restarts during development as well as production builds. #5969
Improved stability when quickly volume-annotating large structures. #6000
The front-end API labelVoxels returns a promise now which resolves as soon as the label operation was carried out. #5955
webKnossos no longer tries to reach a save state where all updates are sent to the backend to be in sync with the frontend when the save is triggered by a timeout. #5999
When changing which layers are visible in an annotation, this setting is persisted in the annotation, so when you share it, viewers will see the same visibility configuration. #5967
Downloading public annotations is now also allowed without being authenticated. #6001
Downloaded volume annotation layers no longer produce zero-byte zipfiles but rather a valid header-only zip file with no contents. #6022
Changed a number of API routes from GET to POST to avoid unwanted side effects. #6023
Removed unused datastore route checkInbox (use checkInboxBlocking instead). #6023
Migrated to Google Analytics 4. #6031

Fixed¶

Fixed volume-related bugs which could corrupt the volume data in certain scenarios. #5955
Fixed the placeholder resolution computation for anisotropic layers with missing base resolutions. #5983
Fixed a bug where ad-hoc meshes were computed for a mapping, although it was disabled. #5982
Fixed a bug where volume annotation downloads would sometimes contain truncated zips. #6009
Fixed a bug where downloaded multi-layer volume annotations would have the wrong data.zip filenames. #6028
Fixed a bug which could cause an error message to appear when saving. #6052

22.02.0 - 2022-01-24¶

Commits

Highlights¶

Added the possibility to add additional volume layers to an existing annotation via the left sidebar. #5881

Added¶

Added a warning when navigating away from editing the dataset's properties without having saved. #5948
Tiff exports are now served from the datastore module to prepare for remote datastores with webknossos-worker. #5942
Added the organization id to the auth token page and organization page. #5965
Added the possibility to cancel running webknossos-worker jobs. #5946
Partially executed floodfills can now be finished by starting a worker job from the bounding box tab (requires a webKnossos instance where jobs are set up). #5905

Changed¶

Improved the UI for automatic suggestions to the datasource properties when editing a dataset. #5948

Fixed¶

Fixed bug where volume data downloads would sometimes produce invalid zips due to a race condition. #5926
Fixed a bug which caused that the keyboard delay wasn't respected properly when rapidly pressing a key. #5947
Fixed that navigating away from uploading a dataset properly warns the user that there is unsaved state. #5948
Fixed a bug where an organization would be created for an already existing email address. #5949
Fixed a bug where the paths of uploaded files were not checked correctly. #5950
Fixed that the used datastore could not be changed in the UI when uploading a dataset. #5952
Fixed the context menu positioning at the bottom and right edges of the screen. #5976

Removed¶

Breaking Changes¶

22.01.0 - 2022-01-04¶

Commits

Highlights¶

Added tagging support for datasets. #5832

Added¶

Dataset upload back-end now supports linking layers of existing public datasets. #5863
Activate the correct mapping before loading pre-computed meshes if the corresponding mesh file contains that information. #5859

Fixed¶

Fixed a bug where dataset uploads that contained files larger than 2 GB failed. #5889
Fixed that dataset uploads did not survive back-end restarts. #5831
Fixed a bug where NMLs with unconnected trees and nested tree groups could not be uploaded due to wrong tree group IDs. #5893
Fixed a security vulnerability by upgrading log4j to the newest version. #5900

Breaking Change¶

When using the front-end API, functions that accept a layer name, such as api.data.getDataValue, won't interpret the name "segmentation" as the current volume tracing if it exists. Instead, "segmentation" can only be used if the current dataset has a layer which is named "segmentation". If you want to interact with the volume tracing layer, use api.data.getVolumeTracingLayerIds() instead. Also see api.data.getSegmentationLayerNames and api.data.getVisibleSegmentationLayer. #5771
The datastore server routes /datasets/reserveUpload and /datasets/finishUpload now expect the additional field layersToLink, which should be an empty list by default. #5863

21.11.2 - 2021-12-21¶

Commits

Fixed¶

Fixed a security vulnerability by upgrading log4j to newest version (2.17.0). #5913

21.11.1 - 2021-12-16¶

Commits

Fixed¶

Fixed a security vulnerability by upgrading log4j to newest version (2.15.0). #5900

21.11.0 - 2021-11-30¶

Commits

Highlights¶

Added a new bounding box tool that allows resizing and creating bounding boxes more easily. Additionally, the context menu now contains options to modify the bounding box close to the clicked position. #5767

Changed¶

The docker setup has been restructured, which requires changes to existing docker-compose setups. See the migration guide for details. #5843
By default, if data is missing in one magnification, higher magnifications are used for rendering. This setting can be controlled via the left sidebar under "Render Missing Data Black". #5862
Made the w shortcut to cycle through the tools non-looping. #5865
The communication with webknossos-worker for long-running jobs no longer uses flower/celery, but instead webKnossos itself assigns jobs to polling workers. #5834

Fixed¶

Fixed a bug that the displayed value range of a histogram of a color layer wasn't applied until the slider was dragged a bit. #5853
Fixed a bug where admins could not share annotations with teams they were not explicitly a member of. #5845

Removed¶

Removed 1 shortcut which allowed to cycle through the tools but only if some of the tools were active. Use w instead. #5865

21.10.0 - 2021-11-08¶

Commits

Highlights¶

A new "Segments" tab was added which replaces the old "Meshes" tab. The tab renders a list of segments within a volume annotation for the visible segmentation layer. The list "grows" while creating an annotation or browsing a dataset. For example, selecting an existing segment or drawing with a new segment id will both ensure that the segment is listed. Via right-click, meshes can be loaded for a selected segment. The mesh will be added as child to the segment. #5696
Enhanced the volume fill tool to so that it operates beyond the dimensions of the current viewport. Additionally, the fill tool can also be changed to perform in 3D instead of 2D. #5733
The active mapping is now included in the link copied from the "Share" modal or the new "Share" button next to the dataset position. It is automatically activated for users that open the shared link. #5738

Added¶

Added the possibility to load the skeletons of specific agglomerates from an agglomerate file when opening a tracing by including a mapping and agglomerate ids in the URL hash. See the docs for further information. #5738
Added a skeleton sandbox mode where a dataset can be opened and all skeleton tracing capabilities are available. However, by default changes are not saved. At any point, users can decide to copy the current state to their account. The sandbox can be accessed at <webknossos_host>/datasets/<organization>/<dataset>/sandbox/skeleton. In the combination with the new agglomerate skeleton loading feature this can be used to craft links that open webknossos with an activated mapping and specific agglomerates loaded on-demand. #5738
For ad-hoc mesh computation and for mesh precomputation, the user can now select which quality the mesh should have (i.e., via selecting which magnification should be used). #5696
The context menu in the data viewport also allows to compute an ad-hoc mesh for the selected segment. #5696

Changed¶

Improved the movement behavior when using shortcuts to navigate along the 3rd dimension. Instead of clamping the sub-voxel position to .0 or .99 on the initial movement, the keyboard delay is adapted dynamically to avoid too fast movements. This change especially improves the move behavior when quickly changing the direction backwards/forwards. #5801

Fixed¶

Fixed two volume tracing related bugs which could occur when using undo with a slow internet connection or when volume-annotating more than 5000 buckets (32**3 vx) in one session. #5728
Jobs status is no longer polled if jobs are not enabled, avoiding backend logging spam #5761
Fixed a bug that windows user could not open the context menu as it instantly closed after opening. #5756.
Fixed a bug where the health check of public datasets failed if no cookie/token was supplied. #5768.
Fixed a bug where retried save requests could lead to a 409 CONFLICT error if the first request was already handled by the back-end. #5779.
Fixed a bug where volume annotations could not be saved under certain circumstances (if "Render Missing Data Black" was disabled and a data bucket was annotated for the first time). #5783
Fixed a bug which made the ad-hoc mesh loading abort too early. #5696
Fixed that viewports turned black when zoomed in very much. #5797
Fixed the bucket loading order in the YZ and XZ viewports. Data in these viewports will be rendered faster than before. #5798
Fixed that collapsing/expanding the sidebars did not work for touchscreens. #5825
Fixed a bug where projects could not be listed if the tracing time got too large. #5823

21.09.0 - 2021-10-01¶

Commits

Highlights¶

Added shortcuts K and L for toggling the left and right sidebars. #5709
Added support for datasets that have multiple segmentation layers. Note that only one segmentation layer can be rendered at a time, currently. #5683

Added¶

Added a rudimentary version of openAPI docs for some routes. Available at /swagger.json. #5693

Changed¶

By default, if data is missing in one magnification, higher magnifications are used for rendering. This setting can be controlled via the left sidebar under "Render Missing Data Black". #5703
Refactor the format of the URL hash/fragment to alternatively use JSON. Old links will continue to work. #5730

Fixed¶

Fixed a bug where existing tasktypes with recommended configurations still had a property that is no longer valid. #5707
Fixed that segment IDs could not be copied to the clipboard. #5709
Fixed a bug where volume annotation version restore skipped buckets that were not yet touched in the version to be restored. #5717
Fixed a rendering bug showing non-existent or wrongly-colored edges that sometimes occurred after deleting edges, nodes, or trees. #5724
Fixed an error during viewport maximization in flight mode. Also, fixed a crash during minimization of the 3D-View for datasets with lots of magnifications. #5746

21.08.0 - 2021-08-26¶

Commits

Highlights¶

Added the possibility to restrict the volume resolutions when creating explorative annotations. Use this to annotate larger structures without creating tons of high-res data. #5645
Most recent dataset conversions are shown in dashboard (if the webKnossos instance supports processing jobs). #5597
Added UI to infer nuclei for webknossos instances that support jobs (e.g., webknossos.org). #5669

Added¶

Fixed a bug where non-existing resolutions could be selected for wk-worker-based meshfile computations #5631
Added new mesh-related functions to the front-end API: getAvailableMeshFiles, getActiveMeshFile, setActiveMeshFile, loadPrecomputedMesh, computeMeshOnDemand, setMeshVisibility, removeMesh. #5634
Added a route to call new webknossos-worker job for nuclei inferral. #5626
Added shortcut information to the context menu. Some shortcuts that are only available for the classic controls are only shown when the classic controls are active. #5677
For webknossos.org, a "What's New" notification was added to the navbar. #5665
Added tooltips for all elements of the Settings tab in the left sidebar. #5673

Changed¶

Improved context menu for interactions with segmentation data that wasn't loaded completely, yet. #5637
Any feature connected to computational jobs like precomputing a meshfile is now disabled for non local hosted datasets. #5663
Clicking outside of the context menu closes it without performing any other action (e.g., previously, a node could be created when clicking outside of the context menu, when the skeleton tool was active). Also, a repeated right-click doesn't open the context menu again. #5658
When the option "Rendering missing data black" is turned of, the fallback data is now shown up to a zoom difference of 3. Previously it was 1. #5674

Fixed¶

Fixed that active segment and node id were not shown in status bar in a non-hybrid annotation. #5638
Fixed that setting an intensity range of a color layer to 0 via the histogram slider led to no data being rendered at all. #5676
Fixed that "Compute Mesh File" button was enabled in scenarios where it should not be supported (e.g., when no segmentation layer exists). #5648
Fixed a bug where an authentication error was shown when viewing the meshes tab while not logged in. #5647
Fixed that segment id 0 was always shown even when fallback data of the segmentation layer was visible and hovered with the mouse. #5674
Fixed that nodes could only be selected via the context menu when an annotation was opened in read-only mode. Shift-Click will now work, too (and if "Classic Controls" are disabled, a simple left click will work, too). #5661
Fixed that the copy buttons in the context menu did not work properly. #5658
Fixed that the position of the mouse displayed in the statusbar was not updated properly when navigating via the keyboard. #5670
Fixed that creating a new node in merger mode did always turn off the "Hide unmapped segments" setting. #5668
Fixed that undo in volume annotations might overwrite the backend data on not loaded magnifications with zeros. #5608
Fixed a bug where volume annotation downloads were occasionally cancelled with “Connection reset by peer” error. #5660
Fixed that the ad-hoc mesh computation was disabled for volume annotations. #5689

Breaking Change¶

The interface of the cross-origin API changed. The initialization message is no longer an object with a message property of "api ready", but instead an object with a type property of "init". Additionally, if an API call finishes, a return message of type "ack" is sent. If the original API call contained a messageId property, the return message will contain the same messageId to allow to match the return message. If the API call is misformatted, a return message of type "err" is sent, containing an error message in the message property.

21.07.0 - 2021-07-21¶

Commits

Highlights¶

Several improvements and changes have been implemented for the toolbar, sidebar and status bar. See the full changelog for all details (grouped under #5384). Alternatively, read the corresponding blog post. The most important changes are:
The toolbar now contains dedicated tools for moving, editing skeletons and erasing volume data.
Right click opens a context menu for all tools, unless "Classic Mode" is enabled in the Settings tab (left sidebar).
The two tabs in the left sidebar "Annotation" and "Dataset" were renamed and restructured to "Layers" and "Settings". Some elements were also moved to other areas, such as the toolbar (e.g., the merger mode) or to dedicated tabs in the right sidebar (e.g., bounding boxes).
The status bar contains additional elements for (editable) information, such as the active tree id (previously positioned in the left sidebar).
Added compatibility with newer JREs, tested with 8, 11 and 14. #5558

Added¶

Added the possibility for admins to set long-running jobs to a “manually repaired” state. #5530
The toolbar contains two additional tools: #5384
one for the skeleton mode (similar to the existing move tool).
one for erasing volume data (similar to right-dragging with the previous brush/trace tool)
Added colored icons to the status entries in the job list. #5572
Back-end side analytics are now sent to events-relay.webknossos.org by default. You can opt out by setting backendAnalytics.uri to empty in your config. 5607

Changed¶

Improve error logging for unhandled rejections. #5575
Improved dragging behavior of trees/groups in the tree tab. #5573
"Center new Nodes" option was renamed to "Auto-center Nodes" and changed to also influence the centering-behavior when deleting a node. #5538
The displayed webKnossos version now omits the parent release name for intermediate builds. #5565
The following changes belong to #5384:
The move tool is only capable of performing movements (its skeleton-functionalities were moved to a dedicated skeleton tool).
(Unless classic mode is enabled:) Right-click opens a context-sensitive menu by default with various actions, such as creating an edge between two nodes. Consequently, important actions which were done via right click previously were changed:
- In the skeleton tool, left click can be used to create, select and move nodes. Also, mere dragging (without hovering a node) moves the active position (similar to the move tool).
- In the trace/brush tool, erasure cannot be performed with right click, anymore. Instead, CTRL + Shift + Left Click works for erasing. Alternatively, selecting the dedicated erase tool also works.
The two tabs in the left sidebar "Annotation" and "Dataset" were renamed and restructured to "Layers" and "Settings".
- "Layers" contains the layers which were previously visible in "Dataset".
- Also, "Layers" contains a dedicated Skeleton layer which handles skeleton-specific settings (e.g., clipping distance).
- "Merger Mode" and "Soma Clicking" were moved to the toolbar (visible when the skeleton tool is selected).
- “Brush Size” was moved to the toolbar (visible when brush or brush-eraser is selected)
- "Controls" and "Viewport options" (previously under "Annotation") and "Data Rendering" (previously under "Dataset") were moved to "Settings".
- The "Bounding Boxes" section in "Annotation" tab was moved to an own tab to the right sidebar.
- The "Mapping" setting was moved to the segmentation layer in the left sidebar.
The status bar contains additional elements for (editable) information, such as the active tree id (previously positioned in the left sidebar).
In some UI elements, text was replaced by icons. An explaining tooltip can be shown by hovering.
The health check at api/health does not longer include checking data/health and tracings/health if the respective local modules are enabled. Consider monitoring those routes separately. #5601
Improved the progress display for dataset uploads. 5616

Fixed¶

Fixed that a disabled "Center new Nodes" option didn't work correctly in merger mode. #5538
Fixed a bug where dataset uploads of zips with just one file inside failed. #5534
Fixed a benign error message when a dataset without a segmentation layer was opened in view mode or with a skeleton-only annotation. #5583
Fixed crashing tree tab which could happen when dragging a node and then switching directly to another tab (e.g., comments) and then back again. #5573
Fixed a bug that the selection of nodes in the skeleton tool was possible for nodes far behind the position and thus prevented creating new nodes. #5624
Fixed that the UI allowed mutating trees in the tree tab (dragging/creating/deleting trees and groups) in read-only tracings. #5573
Fixed "Create a new tree group for this file" setting in front-end import when a group id of 0 was used in the NML. #5573
Fixed a bug that caused a distortion when moving or zooming in the maximized 3d viewport. #5550
Fixed a bug that prevented focusing the login fields when being prompted to login after trying to view a dataset without being logged in.#5521
Fixed a bug that prevented the modal to export data of a bounding box to tiff files to open up. #5624
Fixed that the 3d view content disappeared permanently if the 3d view was resized to not be visible. #5588
Fixed a bug where nested tree groups were messed up during NML upload if “Create a new tree group for this file.“ is selected. #5596

Removed¶

The following changes belong to #5384:
Removed "Highlight hovered cells" setting (highlight on hover will always be done).
The "Volume" tab was removed. The "Mapping" setting was moved to the segmentation layer in the left sidebar. The "segment id" table was removed, as the status bar also contains the information about the hovered cell id.

21.06.0 - 2021-06-01¶

Commits

Highlights¶

Added the possibility to load precomputed meshes from a meshfile via the meshes tab or context menu. #5345
Added the option to hide the plane borders and crosshairs in the 3D viewport. Also, this setting was moved from the "Other" section of the user settings to the 3D viewport. Additionally, added a setting to hide the dataset bounding box in the 3D view. #5440

Added¶

Added an icon to the info tab of a tracing that links to the dataset settings. It's located next to the dataset name. #5462
Upgraded several dependencies including Play framework to 2.8, yielding performance and security improvements. #5515

Changed¶

Active nodes and trees are now highlighted with a background color in the comments tab. #5461
The visibility of meshes can now be toggled via the meshes tab. #5346
When exporting an user bounding box to tiff, the active mapping will now be applied to the exported data, as well. #5474
Changed the layout of the modal that informs the user about the success of task creations and changed the naming schema for the downloadable csv file containing the information about created tasks. #5491

Fixed¶

Fixed that the row selection in the user table wasn't properly preserved when filtering the table and (un)selecting rows. #5486
Fixed a bug where histograms generation failed for tiny datasets. #5458
Fixed a bug where NMLs with huge tree IDs uploaded via back-end produced broken annotations. #5484
Fixed a bug that led to various possible inconsistencies in the dataset settings in the datasource tab, when the inferred datasource properties suggested by the backend were accepted by the user. #5492
Fixed a bug where the upload of multiple NMLs failed if some of them have an organization attribute and others don’t. #5483
Fixed a bug in the application of agglomerate files where the cumsum.json was not used correctly. #5499
Improve loading of precomputed meshes and fix some issues (e.g., deleting a mesh which was still being loaded) which could produce an invalid state. #5519
Fixed an innocuous error toast when opening the dataset import view. #5526
Fixed that creating/editing a volume task type didn't allow submitting the form. #5532

Removed¶

Removed the button to load or refresh the isosurface of the centered cell from the 3D view. Instead, this action can be triggered from the "Meshes" tab. #5440

21.05.1 - 2021-05-05¶

Commits

Highlights¶

Added a dark theme for webKnossos. #5407

Changed¶

The deployment configuration of webKnossos was cleaned up. If you host your own webKnossos instance, be sure to update your config according to the migration guide. #5208

Fixed¶

Fixed a bug where users could see long-running jobs listing of other users #5435
Fixed a rendering bug which occurred when the initial layout had a hidden 3D viewport. #5429
Fixed an incorrect initial camera rotation in the 3D viewport and an incorrect initial zoom value. #5453
Fixed a bug where the task search showed duplicates if a user had multiple instances of a task (as made possible by the transfer functionality). #5456
Fixed a bug where showing active users of a project, and transferring their tasks was broken. #5456

21.05.0 - 2021-04-22¶

Commits

Highlights¶

The layout of the tracing view was revamped. Most notably, the layout now has two well-behaved sidebars (left and right) which can be collapsed and expanded while the remaining space is used for the main data view. Additionally, a status bar was added which shows important information, such as the currently rendered magnification and useful mouse controls. #5279
Added a screenshot of the 3D view when using the screenshot functionality in the tracing view. #5324

Added¶

The names of Task Types and Projects no longer need to be globally unique, instead only within their respective organization. #5334
Upgraded UI library antd to version 4, creating a slightly more modern look and behavior of many UI elements. #5350
Tiff export jobs of volume annotations now show the link back to the annotation in the jobs list. #5378
Added support for flight- and oblique-mode when having non-uint8 dataset layers. #5396

Changed¶

webKnossos is now part of the image.sc support community. #5332
Meshes that are imported by the user in the meshes tab are now rendered the same way as generated isosurface meshes. #5326
In the new REST API version 4, projects are no longer referenced by name, but instead by id. #5334

Fixed¶

Fixed a bug where some values in the project list were displayed incorrectly after pausing/unpausing the project. #5339
Fixed that editing a task type would always re-add the default values to the recommended configuration (if enabled). #5341
Fixed a bug where tasks created from existing volume annotations that did not have a specified bounding box were broken. #5362
Fixed broken search functionality in select components. #5394
Fixed a bug which could cause corrupted trees when CTRL+Rightclick was used in an empty tree. #5385
Fixed a bug in Safari which could cause an error message (which is safe to ignore). #5373
Fixed artifacts in screenshots near the dataset border. #5324
Fixed a bug where the page would scroll up unexpectedly when showing various confirm modals. #5371
Fixed a bug where user changes (email, activation) would show as successful even if they actually failed. #5392
Fixed a bug where dataset uploads were sent to the wrong datastore, and failed. #5404

21.04.0 - 2021-03-22¶

Commits

Highlights¶

Added the possibility to upload datasets without zipping them first. #5137
Added CTRL+Scroll for zooming, which enables pinch-to-zoom on some trackpads. #5224

Added¶

The time spent on a project is now displayed in the project list. #5209
Added the possibility to export binary data as tiff (if long-runnings jobs are enabled). #5195
Added a link to dataset view mode from annotation mode info tab. #5262
Added the possibility to export also volume annotations as tiff (if long-runnings jobs are enabled). #5246
WKW Dataset uploads with missing mag or layer dir no longer fail, instead the paths are automatically added (defaults to color/1). #5285

Changed¶

Measured distances will be shown in voxel space, too. #5240
Improved documentation and inline-help for data import and conversion. #5420

Fixed¶

Fixed a regression in the task search which could lead to a frontend crash. #5267
Fixed a rendering bug in oblique mode. #5289
Fixed a bug where uploading NMLs from dashboard via file picker was inaccessible. #5308

Breaking Change¶

The front-end API methods measurePathLengthBetweenNodes, measureAllTrees and measureTreeLength were changed to return a tuple containing the distance in nm and in vx (instead of only returning the distance in nm). #5240

21.03.0 - 2021-02-24¶

Commits

Highlights¶

The "Meshes" tab was overhauled, so that it displays generated isosurfaces and imported meshes. Generated isosurfaces can be jumped to, reloaded, downloaded and removed. #4917
Before uploading a dataset webKnossos automatically checks whether a conversion and scale are needed. Additionally, the Upload UI was improved. #5081
Support for KNOSSOS cubes data format was removed. Use the webKnossos cuber tool to convert existing datasets saved as KNOSSOS cubes. #5085

Added¶

Added an explicit /signup (or /auth/signup) route. #5091
Added the annotation option "center new nodes" to switch whether newly created nodes should be centered or not. #4150
For webKnossos maintenance, superUsers can now join organizations without being listed as a user there. #5151
Added the possibility to track events for analytics in the backend. #5156

Changed¶

Changed the font to Titillium Web. #5161
Made the isosurface feature in the meshes tab more robust. If a request fails, a retry is initiated. #5102
Support for the old invite links was removed. These contained the organization name in the URL. The new links contain a token (can be generated in the users view). For instances with a single organization the old invite links should still work. #5091
Users are no longer allowed to deactivate their own accounts. #5070
Users are asked to confirm when leaving the dataset upload view while an upload is still running. #5051
Mailer now uses only TLS1.2 instead of JDK default. #5138
Make keyboard-driven movement through the dataset better aligned with the configured move value in certain scenarios. #5201
User experience domains are now separated by organization. #5149
Changed the default request timeouts for standalone datastores and tracingstores to match those of local ones (10000s instead of 75s). #5174

Fixed¶

Fixed a bug where the user could delete teams that were still referenced in annotations, projects or task types, thus creating invalid state. #5108
Fixed a bug where an error occurred when clicking on the hours/week graph in the statistics overview page. #4779
Fixed a bug where the listing of users that have open tasks of a project failed. #5115
Fixed a bug that task scripts weren't correctly re-initialized when a new task was requested. This happened when certain conditions were met. #5199
Fixed some scenarios where the Meshes tab could cause errors (e.g., when the UI was used but no segmentation layer was available). #5142
Fixed a bug where the user (and telemetry) would get a cryptic error message when trying to register with an email that is already in use. #5152
Fixed a bug where default dataset configuration could not be loaded if a dataset was accessed via sharing token #5164
Fixed a bug where viewing a volume task as compound annotation failed for tasks with single instances. #5198

Removed¶

The isosurface setting was removed. Instead, isosurfaces can be generated via the "Meshes" tab. Also note that the Shift+Click binding for generating an isosurface was removed (for now). Please refer to the "Meshes" tab, too. #4917

21.02.1 - 2021-02-03¶

Commits

Fixed¶

Fixed a bug where the listing of users that have open tasks of a project failed. #5115
Fixed shift+clicking isosurfaces in annotations which contain skeletons. #5257

21.02.0 - 2021-01-20¶

Commits

Highlights¶

The dataset import UI was streamlined by making it clearer when automatic suggestions are available for the dataset properties. Previously, these suggestions were applied automatically which could cause some confusion. #4944
Added the possibility to generate skeletons from an HDF5 agglomerate file mapping on-the-fly. With an activated agglomerate file mapping, use Shift + Middle Mouse Click to import a skeleton of the cell into the annotation. Alternatively, use the button in the segmentation tab to import a skeleton of the centered cell into the annotation. #4958

Added¶

Added a context menu via Shift & Right Click that provides easy access to skeleton functionalities and additional information. #4950
Added a cleanup procedure for erroneous uploads, so failed uploads can be retried without changing the dataset name. #4999

Changed¶

Suggestions for the datasource settings of a dataset are no longer applied automatically. They can be applied optionally now. #4944
The brush tool is disabled in low magnifications (magnification 16 and lower) to avoid performance problems when annotating. #5017
The fill tool is disabled in low magnifications (magnification 2 and lower) to avoid producing spotty annotations (caused by needing too much main memory). #5050
Users can now join multiple organizations, admins can now invite users by email address, skipping the manual user activation step. #4984
Dataset Manager role now additionally grants permission to create explorative annotations on all datasets. #5037

Fixed¶

Fixed a bug where importing NMLs failed if they had unescaped greater-than signs inside of attributes. #5003
Mitigate errors concerning localStorage quotas in the datasets dashboard. #5039
Fixed a bug where viewing a dataset via sharingToken crashed. #5047

21.01.0 - 2020-12-21¶

Commits

Highlights¶

The menu for viewing, editing and creating annotations for a dataset in the dashboard was cleaned up a bit. Creating a hybrid (skeleton + volume) annotation is now the default way of annotating a dataset. The other options are still available via a dropdown. #4939

Added¶

Datasets without any layer are now considered unimported. #4959

Changed¶

For 2d-only datasets the view mode toggle is hidden. #4952
Persist the selected overwrite behavior for hybrid and volume annotations. #4962
Backend NML parser now allows NML nodes without radius attribute. Instead, their radius now defaults to a value of 1.0, which is also the new default value for initial nodes. Note that the node radius is only relevant when default setting “overwrite node radius” is disabled. #4982

Fixed¶

Fix crash for trees with high comment count (> 100000 nodes). #4965
Fix the upload of single file datasets. #4977

20.12.0 - 2020-11-23¶

Commits

Highlights¶

Added multi-resolution volume annotations. As a result, volume tracings can be viewed even when zooming out to downsampled magnifications. Note that already existing volume tracings will still only contain data in the first magnification. If you want to migrate an old volume tracing, you can explicitly trigger the downsampling in the sidebar's layer settings. #4755
Improved performance of volume annotations (brush and trace tool). #4848

Added¶

The total length of skeletons can now be measured using the dropdown in the tree list tab. Also, the frontend API received the methods api.tracing.measureTreeLength and api.tracing.measureAllTrees. #4898
Introduced an indeterminate visibility state for groups in the tree tab if not all but only some of the group's children are visible. Before, the visibility of those groups was shown as not visible which made it hard to find the visible trees. #4897
Dataset uploads on a specific Datastore can now be restricted to a single organization. #4892
Added a button to set the color of a tree in the trees tab view. #4907

Changed¶

In the tree tab, all groups but the root group are now collapsed instead of expanded when opening a tracing. #4897
New volume/hybrid annotations are now automatically multi-resolution volume annotations. #4755
Re-enabled continuous brush strokes. This feature ensures that even fast brush strokes are continuous and don't have "holes". #4924
The Histogram now has a correct linear scale. #4926

Fixed¶

Fixed the disappearing of dataset settings after switching between view mode and annotation mode. #4845
Fixed a rare error in the agglomerate mapping for large datasets. #4904
Fixed a bug where in volume annotation zip upload some buckets were discarded. #4914
Fixed the Dataset import which was broken temporarily. #4932
Fixed the upload of multiple volume annotations with similar data zip names. #4915

20.11.0 - 2020-10-26¶

Commits

Highlights¶

Improved the toolbar to make the different webKnossos tools easier to use. For example, the fill-tool and the cell-picker have a dedicated button in volume annotations now. #4875
The dataset upload is now more robust and can recover from a failed upload of a data chunk. #4860
Movements in the 3D viewport are now time-tracked. #4876

Added¶

Hybrid tracings can now be imported directly in the tracing view via drag'n'drop. #4837
The find data function now works for volume tracings, too. #4847
Added admins and dataset managers to dataset access list, as they can access all datasets of the organization. #4862
Added the possibility to move the current position by dragging with the middle-mouse-button (regardless of the active tool). #4875
Sped up the NML parsing via dashboard import. #4872

Changed¶

Brush circles are now connected with rectangles to provide a continuous stroke even if the brush is moved quickly. #4785
The position input of tracings now accepts decimal input. When losing focus the values are cut off at the comma. #4803
webknossos.org only: Accounts associated with new organizations can now be created even when a datastore is unreachable. The necessary folders are created lazily when needed. #4846
When downloading a volume tracing, buckets containing a single 0 byte, that were created to restore older versions, are now skipped. #4851
Task information CSV now contains additional column creationInfo, containing the original NML filename for tasks based on existing NMLs. #4866
The default overwrite-behavior in volume annotating changed so that erasing with the brush- or trace-tool always erases all voxels (regardless of their segment id). Before that, only the current segment id was overwritten by default. As before, this behavior can be toggled by pressing CTRL. Alternatively, one can now also switch the mode in the toolbar. #4875

Fixed¶

Fixed failing histogram requests for float layers with NaN values. #4834

20.10.0 - 2020-9-21¶

Commits

Highlights¶

Added the possibility to undo and redo volume annotation strokes. #4771
Isosurface generation now also supports volume tracings (without fallback layers). #4567
Added a tool to initiate a flood fill in a volume tracing with the active cell id. #4780
Added the possibility to navigate to the preceding/subsequent node by pressing "ctrl + ," or "ctrl + ." in a skeleton tracing. #4147

Added¶

Added the possibility to merge volume tracings both via file upload (zip of zips) and when viewing projects/tasks as compound annotations. #4709
Added the possibility to remove the fallback segmentation layer from a hybrid/volume tracing. Accessible by a minus button next to the layer's settings. #4741

Changed¶

When d/f switching is turned off and a slice is copied with the shortcut v, the previous slice used as the source will always be slice - 1 and shift + v will always take slice + 1 as the slice to copy from. #4728
Disabled the autofill feature of the brush when using this tool to erase data. #4729
The rotation buttons of the 3D-viewport no longer change the zoom. #4750
Improved the performance of applying agglomerate files. #4706
When uploading tasks via NML, NML are shown in the task modal instead of a toast. #4723

Fixed¶

Improved the data loading behavior for flight and oblique mode. #4800
Fixed an issue where in some cases the tree list was only visible after the window was resized. #4816
Fixed a bug where some volume annotations that had been reverted to a previous version became un-downloadable. #4805
Fixed a UI bug where some tooltip wouldn't close after editing a label. #4815

20.09.0 - 2020-8-20¶

Commits

Highlights¶

Improved the distinguishability of segments by improving the color generation and also by rendering patterns within the segments. The pattern opacity can be adapted in the layer settings (next to the opacity of the segmentation layer). #4730
Added the possibility to move nodes in skeleton tracings. This can be done either by pressing CTRL + arrow key or by dragging while holding CTRL. #4743

Added¶

Added the possibility to delete datasets on disk from webKnossos. Use with care. #4696
Added error toasts for failing bucket requests. #4740
Added a list of all projects containing tasks of a specific task type. It's accessible from the task types list view. #4420

Changed¶

When d/f switching is turned off and a slice is copied with the shortcut v, the previous slice used as the source will always be slice - 1 and shift + v will always take slice + 1 as the slice to copy from. #4728
Disabled the autofill feature of the brush when using this tool to erase data. #4729
The rotation buttons of the 3D-viewport no longer change the zoom. #4750
Improved the performance of applying agglomerate files. #4706
In the Edit/Import Dataset form, the "Sharing" tab was renamed to "Sharing & Permissions". Also, existing permission-related settings were moved to that tab. #4683
Improved rotation of camera in 3D viewport. #4768
Improved handling and communication of failures during download of data from datasets. #4765
The volume annotation tools in hybrid tracings are disabled while in merger mode. #4757
The title of a tab now shows the active tracing or dataset as well as the corresponding organization. #4653
When viewing or tracing a dataset with only one slice (2D data) the default layout displays only the XY plane. The other viewports can still be accessed by changing the viewport tab. #4738

Fixed¶

Speed up NML import in existing tracings for NMLs with many trees (20,000+). #4742
Fixed tree groups when uploading NMLs with multi-component trees. #4735
Fixed that invalid number values in slider settings could crash webKnossos. #4758
Improved resilience in time tracking, preventing overlapping timespans. #4830

20.08.0 - 2020-07-20¶

Commits

Highlights¶

Added the possibility to have multiple user-defined bounding boxes in an annotation. Task bounding boxes are automatically converted to such user bounding boxes upon “copy to my account” / reupload as explorational annotation. #4536
Separated the permissions of Team Managers (now actually team-scoped) and Dataset Managers (who can see all datasets). The database evolution makes all Team Managers also Dataset Managers, so no workflows should be interrupted. New users may have to be made Dataset Managers, though. For more information, refer to the updated documentation. #4663
Backend NML parser no longer rejects NMLs with trees that have multiple connected components. Instead, it splits those into one separate tree per component. #4688

Added¶

Added the possibility to adjust the minimum and maximum value of the histogram for a layer. This option can be opened in the top right corner of the histogram. #4630
Added a warning to the segmentation tab when viewing uint64 bit segmentation data. #4598
Added the possibility to have multiple user-defined bounding boxes in an annotation. Task bounding boxes are automatically converted to such user bounding boxes upon “copy to my account” / reupload as explorational annotation. #4536
Added additional information to each task in CSV download. #4647
Added the possibility to configure the sender address used in emails wk sends (mail.defaultSender in application.conf). #4701
Added a warning during task creation if task dataset cannot be accessed by project team members. #4695
Included the server time in error messages, making debugging misbehavior easier. #4707

Changed¶

Separated the permissions of Team Managers (now actually team-scoped) and Dataset Managers (who can see all datasets). The database evolution makes all Team Managers also Dataset Managers, so no workflows should be interrupted. New users may have to be made Dataset Managers, though. For more information, refer to the updated documentation. #4663
Refined all webKnossos emails for user signups etc. Switched emails to use HTML templates for more bling bling. #4676
Backend NML parser no longer rejects NMLs with trees that have multiple connected components. Instead, it splits those into one separate tree per component. #4688

Fixed¶

Fixed that merger mode didn't work with undo and redo. Also fixed that the mapping was not disabled when disabling merger mode. #4669
Fixed a bug where webKnossos relied upon but did not enforce organization names to be unique. #4685
Fixed that being outside of a bounding box could be rendered as if one was inside the bounding box in some cases. #4690
Fixed a bug where admins could revoke their own admin rights even if they are the only admin in their organization, leading to an invalid state. #4698
Fixed a bug where webKnossos ignored existing layer category information from datasource-properties.json when exploring layers on disk. #4694

Removed¶

Removed the “are you sure” warning when editing datasets with no allowed teams. Instead, a warning during task creation is shown in this case. #4695

20.07.0 - 2020-06-29¶

Commits

Highlights¶

Fixed that the dataset list in the dashboard could reorder its items asynchronously which could be very annoying for the user. #4640

Added¶

Added a warning to the segmentation tab when viewing uint64 bit segmentation data. #4598

Changed¶

The redundant “team” column was removed from the bulk task creation format. #4629
The brush size minimum was changed from 5 voxels to 1. #4648

Fixed¶

Fixed that the dataset list in the dashboard could reorder its items asynchronously which could be very annoying for the user. #4640
Improved resilience when refreshing datasets while a datastore is down. #4636
Fixed a bug where requesting volume tracing fallback layer data from webknossos-connect failed. #4644
Fixed a bug where imported invisible trees were still visible. #4659
Fixed the message formatting for standalone datastores and tracingstores. #4656

20.06.0 - 2020-05-25¶

Commits

Highlights¶

Compression of volume tracing data is now already done in the browser, reducing I/O load and required disk space. #4602 and #4623

Added¶

Added the possibility to select hour, minute and second of the time range in the timetracking view. #4604
Volume tracing data is now saved with lz4 compression, reducing I/O load and required disk space. #4602
Volume tracing data is now already lz4-compressed in the browser, further reducing server load. #4623

Changed¶

Improved the UI in navigation bar during loading of tracings and datasets. #4612
Improved logging in case of very slow annotation saving. Additionally, the user is also warned when there are unsaved changes older than two minutes. #4593
REST API for creating / changing datastores now contains additional field allowsUpload denoting if the datastore allows uploading datasets via browser. #4614

Fixed¶

When activating an agglomerate file-based ID mapping, only the segmentation layer will be reloaded from now on. This will improve mapping activation performance. #4600
Fixed retrying of failed save requests sent during tracingstore restart. #4591
Fixed the initial loading of agglomerate mappings, where some buckets remained black. #4601
Fixed occasional error during loading of compound annotations (such as viewing multiple finished task instances in one view). #4619

20.05.0 - 2020-05-05¶

Commits

Highlights¶

Added support for ID mapping of segmentation layer based on HDF5 agglomerate files. #4469
Added option to hide all unmapped segments to segmentation tab. #4510
It is now possible to upload volume tracings as a base for tasks. The upload format is similar to the project / task type download format. #4565
Added the possibility to share the dataset which is currently viewed (using a private token if the dataset is not public). The option can be found in the dropdown of the navigation bar. #4543

Added¶

Users can undo finishing a task when the task was finished via the API, e.g. by a user script. #4495
Added the magnification used for determining the segment ids in the segmentation tab to the table of the tab. #4480
Added support for ID mapping of segmentation layer based on HDF5 agglomerate files. #4469
Added the possibility to share the dataset which is currently viewed (using a private token if the dataset is not public). The option can be found in the dropdown of the navigation bar. #4543
Added option to hide all unmapped segments to segmentation tab. #4510
When wK changes datasource-properties.json files of datasets, now it creates a backup log of previous versions. #4534
Added a warning to the position input in tracings if the current position is out of bounds. The warning colors the position input orange. #4544
Isosurface generation now also supports hdf5-style mappings. #4531

Changed¶

Reported datasets can now overwrite existing ones that are reported as missing, this ignores the isScratch precedence. #4465
Improved the performance for large skeleton tracings with lots of comments. #4473
Users can now input floating point numbers into the rotation field in flight and oblique mode. These values will get rounded internally. #4507
Deleting an empty tree group in the Trees tab no longer prompts for user confirmation. #4506
Toggling the "Render missing data black" option now automatically reloads all layers making it unnecessary to reload the whole page. #4516
The "mappings" attribute of segmentation layers in datasource jsons can now be omitted. #4532
Uploading a single nml, allows to wrap the tracing in a new tree group. #4563
Unconnected trees no longer cause an error during NML import in the tracing view. Instead, unconnected trees are split into their components. The split components are wrapped in a tree group with the original tree's name. #4541
Made the NML importer in the tracing view less strict. Incorrect timestamps, missing tree names or missing node radii no longer cause an error. #4541
Disabled the backend-side apply agglomerate feature for downsampled magnifications (still allowed for 1 to 8) to save server capacity. #4578
REST API endpoints finish and info now expect additional GET parameter timestamp=[INT] timestamp in milliseconds (time the request is sent). #4580
It is now possible to upload volume tracings as a base for tasks. The upload format is similar to the project / task type download format. #4565

Fixed¶

Users only get tasks of datasets that they can access. #4488
Ignoring an error message caused by the drag and drop functionality. This error claims that a reload of the tracing is required although everything is fine. #4544
Fixed that after selecting a node in the 3d viewport the rotating center of the viewport was not updated immediately. #4544
Fixed the import of datasets which was temporarily broken. #4497
Fixed the displayed segment ids in segmentation tab when "Render Missing Data Black" is turned off. #4480
The datastore checks if a organization folder can be created before creating a new organization. #4501
Fixed a bug where under certain circumstances groups in the tree tab were not sorted by name. #4542
Fixed that segmentationOpacity could not be set anymore as part of the recommended settings for a task type. #4545
Fixed registration for setups with one organization and not configured defaultOrganization. #4559
Fixed a rendering error which could make some layers disappear in certain circumstances. #4556
Fixed a rendering error which caused negative float data to be rendered white. #4556
Fixed the histogram creation if some sampled positions don't contain data. #4584
Fixed a rendering exception which could occur in rare circumstances. #4588

20.04.0 - 2020-03-23¶

Commits

Highlights¶

Added the possibility to reopen finished tasks as non-admin for a configurable time. #4415
Added support for drag-and-drop import of NML files even if the current view is read-only (e.g., because a dataset was opened in "view" mode). In this case, a new tracing is directly created into which the NML file is imported. #4459
Added support for setting view configuration defaults in the datasource-properties.json. Use the defaultViewConfiguration field for Dataset settings and the defaultViewConfiguration field inside a layer for layer-specific settings. #4357

Added¶

Added support for setting view configuration defaults in the datasource-properties.json. Use the defaultViewConfiguration field for Dataset settings and the defaultViewConfiguration field inside a layer for layer-specific settings. #4357
Added a notification when downloading nml including volume that informs that the fallback data is excluded in the download. #4413
Added the possibility to reopen finished tasks as non-admin for a configurable time. #4415
Added support for drag-and-drop import of NML files even if the current view is read-only (e.g., because a dataset was opened in "view" mode). In this case, a new tracing is directly created into which the NML file is imported. #4459
Added download of task configurations as CSV after task creation and in the task list view. #4491
Added indication for reloading a dataset in the dataset actions in the dashboard. #4421
Added support for creating a tree group when importing a single NML into an existing annotation. #4489
Added login prompt to the tracing page when fetching the dataset fails. Upon successful login, the dataset gets fetched with the rights of the newly logged-in user. #4467

Changed¶

Changed NML import in tracings to try parsing files as NMLs and protobuf regardless of the file extension. #4421
Using the "Best Quality First" strategy in combination with having the "Render Black Data" setting disabled works better now. #4470
Default interval for detecting new/deleted datasets on disk has been reduced from 10 to 1 minute. #4464
The config values datastore.publicUri, tracingstore.publicUri and http.uri are now reapplied from the config at every startup if your instance has localhost-stores #4482

Fixed¶

Fixed that a node was created when using right click while brushing mode is active in hybrid tracings. #4433
Fixed opening view only dataset links with arbitrary modes being initially displayed in plane mode. #4421
Fixed that converting a volume tracing into a hybrid tracing opens the hybrid tracing in "volume" mode. #4467
Fixed a bug where users were wrongly allowed to edit the description of an annotation they were allowed to see but not update #4466
Fixed the creation of histograms for float datasets that only have one value besides 0. #4468
Fixed the creation of histograms for float datasets that have values close to the minimum. #4475
Fixed the import of datasets which was temporarily broken. #4497

Removed¶

-

20.03.0 - 2020-02-27¶

Commits

Highlights¶

Added support for datasets with more layers than the hardware can render simultaneously. The user can disable layers temporarily to control for which layers the GPU resources should be used. #4424
Time tracking precision is improved. #4445

Added¶

Added support for datasets with more layers than the hardware can render simultaneously. The user can disable layers temporarily to control for which layers the GPU resources should be used. #4424
Added a notification when downloading nml including volume that informs that the fallback data is excluded in the download. #4413
Added a simpler method to install webKnossos on an own server. #4446

Changed¶

Made the navbar scrollable on small screens. #4413
Opening the settings sidebar when viewing a dataset or tracing defaults to the dataset settings now. #4425
Better onboarding experience for new users on webknossos.org. #4439

Fixed¶

Fixed that for uint16 data layer the default value range of [0, 255] was used, causing most of the data to look white without manual adjustments. Now the correct range of [0, 65535] is used as default. #4381
Time tracking precision is improved. #4445

Removed¶

-

20.02.0 - 2020-01-27¶

Commits

Added¶

Added new viewing permission for annotations: public (everyone with the link has access, logged in or not), internal (everyone from your organization has access), private (only you and your team managers and admins have access). The new default is internal as it is the old default non-public.
Added support for using task ids as base for a new task, if the corresponding task only has one (finished) instance. #4404

Changed¶

Changed the error message when importing a dataset without resolution directories. #4389

Fixed¶

Fixed the deactivation of datasets if no datasets are present. #4388
Fixed the team sharing settings for private annotations. #4409
Fixed the team sharing loading for read only tracings. #4411
Fixed the renaming of annotations in the tracing view. #4416

20.01.0 - 2020-01-08¶

Commits

Highlights¶

Added a scale to the y-axis of histograms to indicate the logarithmic representation. Additionally, small histogram values are smoothed out. #4349
You can now share your annotations with selected teams. These annotations appear in the Shared Annotations Tab in the dashboard. #4304

Added¶

Added publicUri configs for datastore and tracingstore for initial setup. #4368
Added a button to delete all cached data buckets of color layer and the reload them. #4383
Added a scale to the y-axis of histograms to indicate the logarithmic representation. Additionally, small histogram values are smoothed out. #4349
Added a new way of sharing annotations. You can share your annotations with selected teams. These annotations appear in the Shared Annotations Tab in the dashboard. #4304
Added an option to invert the color values of color layers. #4382

Changed¶

Changed the way the new active tree is selected after deleting a tree. Now the tree with the next highest id, compared to the id of the deleted tree, is selected. #4370
Consolidates URI handling in the config. Pairs of uri and secured entries are now specified as just uri and require either http:// or https:// prefix. #4368
Renamed initial organization for the dev deployment to sample_organization. #4368

Fixed¶

Fixed an issue where webKnossos would complain in certain scenarios when resolutions of datasets were not complete. #4344
Fixed permissions to all task lists, so only administrable tasks can get accessed. #4331

19.12.0 - 2019-11-25¶

Commits

Highlights¶

Added possibility to disable saving in an explorative annotation. This feature can save a lot of resources when dealing with very large NMLs which don't need to be persisted. #4321
Added support for importing tracings in a binary protobuf format via drag and drop. #4320
Fixed broken sorting in the dataset table of the dashboard. #4318

Added¶

Added support for importing tracings in a binary protobuf format via drag and drop. #4320
Added an API to set a tree active by name. #4317
Added possibility to disable saving in an explorative annotation. This feature can save a lot of resources when dealing with very large NMLs which don't need to be persisted. #4321

Changed¶

Some user actions, like deleting a group with all subtrees, resulted in lots of entries in the undo stack (one for each deleted tree). Those actions are now handled as a single atomic change and can be undone with a single undo invocation. #4312
The "Find Data" feature will jump to the center of the layer's bounding box, if no data could be found. The "Find Data" feature can be found next to each layer's name in the dataset settings tab. #4346

Fixed¶

Fixed broken sorting in the dataset table of the dashboard. #4318
Fixed annotation access to match the text in the modal. #4314
Fixed that the brush tool could be selected in an read-only tracing. #4345
Fixed the name of downloaded annotation zips. #4330

19.11.0 - 2019-10-28¶

Commits

Added¶

Added an API to manage DataStores and TracingStores as admin. #4286

Fixed¶

Cleaned up error reporting wording in case of dataset access failures (e.g. due to not being logged in). #4301
Fixed handling of uint64 data layers in sql evolution. #4303

19.10.0 - 2019-09-30¶

Commits

Highlights¶

Clicking on an experience domain of a user, while multiple users are selected will edit the domain of all selected users (instead of only the domain of the clicked row). #4280
Creating a new skeleton tree group will always activate that group. #4282
Resetting a task to the initials state is now also allowed for volume tasks. #4276

Added¶

Reset to base is now also allowed for volume tasks. #4276

Changed¶

Renamed "Expected Time" to "Time Limit" in the project table. #4278
Clicking on an experience domain of a user, while multiple users are selected will edit the domain of all selected users (instead of only the domain of the clicked row). #4280
Creating a new skeleton tree group will always activate that group. #4282

Fixed¶

When creating tasks from zip, the individual nml names are used again, rather than the zip name. #4277

Removed¶

Removed the Search shortcut (Ctrl+Shift+F) for comments in the tracing view, since that shortcut collides with the tree search. #4291

19.09.0 - 2019-08-28¶

Commits

Highlights¶

Users can see their own time statistics now. #4220
Added limited support for uint64 segmentation layer by using the lower 4 bytes. #4233
Added a scale bar to the 3D viewport. #4258
Added currently spent hours on a project to the project progress view. #4236

Added¶

Added the possibility to have an existing annotation as a base for a new task, thus making it also possible to have a base tracing for volume tasks. #4198
Indicating active nml downloads with a loading icon. #4228
Added possibility for users to see their own time statistics. #4220
Added merger mode as a setting for task types. Enabling this setting will automatically activate merger mode in tasks. #4269
The segmentation layer can now be turned invisible and also supports the find data feature. #4232
Enabled the advanced search for the comment tab. #4238
Added limited support for uint64 segmentation layer by using the lower 4 bytes. #4233
Added an API route to add and delete dataStores. #4242
Added a scale bar to the 3D viewport. #4258
Added the possibility to import an nml file as a string and to reset the active skeleton tracing to the API. #4252
Added currently spent hours on a project to the project progress view. #4236

Changed¶

Each of the columns of the dataset table and explorative annotations table in the dashboard now have an individual fixed width, so the tables become scrollable on smaller screens. #4207
When uploading a zipped annotation (such as volume / hybrid / collection), the zip name is used for the resulting explorative annotation, rather than the name of the contained NML file. #4222
Color and segmentation layer are not longer treated separately in the dataset settings in tracing/view mode. #4232

Fixed¶

Data for disabled or invisible layers will no longer be downloaded, saving bandwidth and speeding up webKnossos in general. #4202
Fixed tooltip not disappearing in the statistics view in certain circumstances. #4219
Fixed the error messages when trying to access a dataset with insufficient permissions. #4244
Fixed the upload of volume tracings by recognizing the correct format of the fallback layer. #4248
Fixed an imprecision when exporting an NML via the front-end. #4262
Fixed viewing and tracing of datasets which only contain a segmentation layer. #4265

19.08.0 - 2019-07-29¶

Commits

Highlights¶

Added the possibility to remove isosurfaces from the 3D viewport by CTRL+Clicking it. #4185
Added support for int16 and uint16 color layers. #4152
Team managers and admins can now get tasks that they had previously cancelled. #4088
Increased performance for time logging. #4196

Added¶

Volume tasks with only one finished instance can now be viewed as CompoundTask. #4167
Added the possibility to remove isosurfaces from the 3D viewport by CTRL+Clicking it. #4185
Added support for int16 and uint16 color layers. #4152
Added histogram support for int16 and uint16 color layers. Additionally refined support for float color layers. #4195

Changed¶

Volume project download zips are reorganized to contain a zipfile for each annotation (that in turn contains a data.zip and an nml file). #4167
Team managers and admins can now get tasks that they had previously cancelled. #4088
Recording is now automatically turned off when switching from flight/oblique to orthogonal mode to prevent accidental node creation when switching back later. #4211

Fixed¶

Fixed a bug where volume tracings could not be converted to hybrid. #4159
Fixed a bug where for uint24 color layers, scrambled data was shown for missing magnifications. #4188
Fixed a bug where collapsing/expanding all tree groups would trigger when toggling a single tree #4178
Fixed performance for time logging. #4196
Personal tracing layouts are saved per user now. #4217
Fixed an error message when quickly resizing the browser window. #4205

Removed¶

-

19.07.0 - 2019-07-01¶

Commits

Highlights¶

Added a histogram and min- / max-sliders to the dataset settings for each layer. This replaces the brightness and contrast settings. #4105
Added the possibility to enforce a certain magnification range for tasks (can be configured in the corresponding task type). #4101
Added the possibility for admins to add experience domains while creating new tasks. #4119

Added¶

Added the possibility to enforce a certain magnification range for tasks (can be configured in the corresponding task type). #4101
Added the possibility for admins to add experience domains while creating new tasks. #4119
Added a histogram to the dataset settings for each layer. It simplifies adjusting the brightness and contrast of a layer and replaces the brightness and contrast slider. #4105
The dataset and the explorative annotations table in the dashboard are now horizontally scrollable if the window is not wide enough. Additionally, clicking on the name of a dataset in the dataset table opens the dataset in view mode. #4136
Added an two additional buttons to the dropdown menu of the tree hierarchy view. On Click, one collapses the other expands all subgroups. #4143

Changed¶

The tooltip of the timeline chart in the Time Tracking view now displays the duration in minutes:seconds. #4121
Reactivated and renamed the "Quality" setting to "Hardware Utilization". Using a higher value will render data in higher quality, but puts more stress on the user's hardware and bandwidth. #4142

Fixed¶

Fixed that team managers couldn't view time tracking details of other users anymore. #4125
Fixed the positioning of the tooltip of the timeline chart in the Time Tracking view. #4121
Fixed a rendering problem which caused a red viewport on some Windows machines. #4133

Removed¶

The brightness and contrast slider in the dataset got removed in favour of the new histogram feature. #4105

19.06.0 - 2019-05-27¶

Commits

Highlights¶

The time tracking view now displays dates instead of hours when having more than one day selected. #4028
BossDB datasets can now be added to webKnossos using the webknossos-connect service. #4036
When holding CTRL while toggling the visibility of a layer, that layer will be made exclusively visible. #4061

Added¶

Non-admin users now can see their own tracing time statistics. #4028
The extent of a dataset is now displayed next to the scale in the dataset list in the dashboard. #4058
BossDB datasets can now be added to webKnossos using the webknossos-connect service. #4036
Added an auto-brush feature for selected datasets. #4053
When holding CTRL while toggling the visibility of a layer, that layer will be made exclusively visible. This change makes it easier to quickly compare different data layers against each other. #4061

Changed¶

Heavily improved mapping creation/activation performance. #4103
The NML parser now rounds floating point values in node coordinates. #4045
The time tracking view now displays dates instead of hours when having more then one day selected. The display id's in the timeline diagram are not the task ids. The tooltip of the timeline diagram also got a rework. #4028
Improved the editing of datasets. Changes suggested by webKnossos will be easier to recognize as suggestions. 4104
The time tracking view now displays dates instead of hours when having more than one day selected. The display id's in the timeline diagram are not the task ids. The tooltip of the timeline diagram also got a rework. #4028

Fixed¶

Fixed an issue where the 3D view was not rendered correctly after maximizing another pane. #4098
The admin task list now only shows tasks belonging to a project one can administrate. #4087
When making a hybrid tracing from a volume tracing, the user bounding box is no longer lost. #4062

Removed¶

It is no longer possible to scroll through planes while dragging one. #4085

19.05.0 - 2019-04-29¶

Commits

Changed¶

Improved performance for large tracings. #3995
Improved how the rendering quality can be adapted in the settings. The setting can now be used to tune the quality to your hardware specification. #4015
Empty trees in skeleton tracings are now allowed. #4010
Creating a hybrid tracing now asks whether to use the existing segmentation layer or use a new one. #4033

Fixed¶

Fixed a missing redirect after registering for an existing organization (with autoVerify=true) via the onboarding flow. #3984
Fixed rendering artifacts which could occur under certain conditions. #4015
Fixed that the zoom step was reset after switching to a new task. #4049

19.04.0 - 2019-04-01¶

Commits

Highlights¶

This release multiple new interactions are expanding webKnossos: - Added merger mode for skeleton and hybrid tracings. It allows to merge segments from e.g. generated oversegmentations. #3619 - Added a shortcut (Q) and button to screenshot the tracing views. #3834 - Rendered isosurfaces in the 3D viewport can now be interacted with. Shift+Click on an isosurface will jump exactly to where you clicked. Also, hovering over an isosurface will highlight that cell in all viewports. #3858 - Neuroglancer precomputed datasets can now be added to webKnossos using the webknossos-connect service. #3843

Also the data viewing and tracing workflow is smoothed further: - Different loading strategies are now supported ("best quality first" and "progressive quality"). Additionally, the rendering can use different magnifications as a fallback. #3801 - Performance improvements #3880 & #3902

Added¶

Rendered isosurfaces in the 3D viewport can now be interacted with. Shift+Click on an isosurface will jump exactly to where you clicked. Also, hovering over an isosurface will highlight that cell in all viewports. #3858
webKnossos now comes with a list of sample datasets that can be automatically downloaded and imported from the menu. #3725
Added a shortcut (Q) and button in the actions dropdown to screenshot the tracing views. The screenshots will contain everything that is visible in the tracing views, so feel free to disable the crosshairs in the settings or toggle the tree visibility using the (1) and (2) shortcuts before triggering the screenshot. #3834
Neuroglancer precomputed datasets can now be added to webKnossos using the webknossos-connect (wk-connect) service. To setup a wk-connect datastore follow the instructions in the Readme. Afterwards, datasets can be added through "Add Dataset" - "Add Dataset via wk-connect". #3843
Added support for mappings for 8-bit and 16-bit segmentation layers. #3953
The dataset settings within the tracing view allow to select between different loading strategies now ("best quality first" and "progressive quality"). Additionally, the rendering can use different magnifications as a fallback (instead of only one magnification). #3801
The mapping selection dropdown is now sorted alphabetically. #3864
Added the possibility to filter datasets in the dashboard according to their availability. By default, datasets which are missing on disk (e.g., when the datastore was deleted) are not shown anymore. This behavior can be configured via the settings icon next to the search box in the dashboard. #3883
Added merger mode for skeleton and hybrid tracings. It allows to merge segments from e.g. generated segmentations. #3619
The HTML template now includes SEO tags for demo instances and hides internal instances from search engines.
Segmentation ID mappings can now be used in volume and hybrid tracings. #3949
A maximize-button was added to the viewports in the annotation view. Maximization can also be toggled with the . shortcut. #3876
webknossos-connect now starts with webKnossos on local and development instances by default. #3913
The visibilities of trees in a skeleton tracing is now persisted across page loads. #3942
Added a button for each color layer to enable/disable the layer. #3943
Paginated routes now send a X-Total-Count HTTP header which shows how many entries were found in total. #3899

Changed¶

Improved the flight mode performance for tracings with very large trees (>80.000 nodes). #3880
Tweaked the highlighting of the active node. The inner node looks exactly as a non-active node and is not round, anymore. An active node is circled by a "halo". In arbitrary mode, the halo is hidden and the active node is round. #3868
Improved the performance of moving through a dataset which should make the overall interaction smoother. #3902
Brush size is independent of zoom value, now. This change simplifies volume annotations, as brush sizes can be adapted to certain structures (e.g., vesicles) and don't need to be changed when zooming. #3868
Reworked the search in the trees tab. #3878

Fixed¶

Fixed a bug where failed large save requests lead to inconsistent tracings on the server. #3829
Fixed the setting which enables to hide the planes within the 3D viewport. #3857
Fixed a bug which allowed the brush size to become negative when using shortcuts. #3861
Fixed interpolation along z-axis. #3888
Fixed that the halo of the active node could cover other nodes. #3919
Fixed that the 3D viewport was partially occluded due to clipping distance issues. #3919
Fixed that scrolling with the mouse wheel over a data viewport also scrolled the page. This bug appeared with the new Chrome version 73. #3939

Removed¶

Removed FPS meter in Annotation View. #3916

19.03.0 - 2019-03-04¶

Commits

Highlights¶

The tracing view got two major improvements:
Data rendering is now fully using the available space and doesn't have to be quadratic anymore. Increasing the size of a viewport will result in more data being rendered (as opposed to the same data will be upscaled). #3634
The active node is highlighted with a "halo ring". Additionally, the node is also rendered as a circle. In flight and oblique modes the halo is hidden. #3731
Added the possibility to create volume annotation tasks. When creating a task type, select whether to create volume or skeleton tasks. Compound viewing and file upload for volume tasks is not yet supported. #3712
Mappings for segmentations will be read automatically from the file system. It's not necessary to define the mappings within the datasource-properties.json anymore. #3720

Added¶

Added the possibility to create volume annotation tasks. When creating a task type, select whether to create volume or skeleton tasks. Note that compound viewing for volume tasks is not supported yet. Same for creating volume tasks from uploaded nml/data files. #3712
Added an UI to select a mapping for a segmentation layer. The UI is placed in the segmentation tab within the tracing view. #3720
Added a button to jump to actual data if the bounding box of a dataset contains a lot of black data. #3682

Changed¶

Data rendering is not tied to square viewports, anymore. As a result the screen space is used more efficiently to show data. Also, increasing the size of a viewport will result in more data being rendered (as opposed to the same data will be upscaled). #3634
Mappings for segmentations will be read automatically from the file system. It's not necessary to define the mappings within the datasource-properties.json, anymore. #3720
The active node is highlighted with a "halo ring". Additionally, the node is also rendered as a circle. In flight and oblique modes the halo is hidden. #3731
In the dashboard list of active tasks, the project name is now featured more prominently, as it switched places with the task type summary. #3792
Isosurfaces are now loaded from the middle outwards. #3818
The brush size will now be remembered across page reloads. #3827
Do not show publication view if no publications are specified. #3778

Fixed¶

Fixed an error that occurred when changing the URL hash. #3746
Fixed a bug in the timeline chart rendering. The start and end time of the timeline chart now match the selected time range. #3772
The modals for a new task description and recommended task settings are no longer shown in read-only tracings. #3724
Fixed a rendering bug when opening a task that only allowed flight/oblique mode tracing. #3783
Fixed a bug where some NMLs caused the webKnossos tab to freeze during NML upload. #3758
Fixed a bug where some skeleton save requests were wrongly rejected if they were sent more than once. #3767
Fixed a bug which caused a wrong aspect ratio in the 3D viewport when changing the layout. #3817

19.02.0 - 2019-02-04¶

Commits

Highlights¶

The Dataset Gallery was redesigned to be a Publication Gallery instead. It will feature scientific publications together with their published datasets and information such as the species, brain region or acquisition method of such datasets. #3653 Please see the migration guide on how to add publications.
Also, this release includes new features that enrich the view of your data:
Isosurface computation can now be triggered for whole segments (shift + click on a segment in view mode). #3655
Added the possibility to fade the alpha value of data layers. Also, a dataset can now contain both RGB and grayscale layers. #3670
The volume annotation brush tool will now automatically fill any enclosed areas if the brushed outline is closed in one stroke. #3698

Added¶

Added the possibility to fade the alpha value of data layers. Also, a dataset can now contain both RGB and grayscale layers. #3670
Added the possibility to disable that the current layout is saved automatically when changing it. Instead, the layout can be saved explicitly. #3620
Added the possibility to use flight and oblique mode when viewing a dataset. #3644
Added pagination to the REST API route GET /projects/:name/tasks (new optional parameters limit and pageNumber). #3659
Added the possibility to open the version restore view for read-only tracings. Older versions can be previewed and be downloaded as NML. #3660

Changed¶

Team managers are now also allowed to create and own scripts. #3676
The Dataset Gallery was redesigned to be a Publication Gallery instead. It will feature scientific publications together with their published datasets and information such as the species, brain region or acquisition method of such datasets. #3653
Annotations for non-public datasets can now be shared using the "Share" functionality without making the dataset public. #3664
The volume annotation brush tool will now automatically fill any enclosed areas if the brushed outline is closed in one stroke. #3698
Statistics are now separated by organization, rather than showing the webKnossos instance’s totals. #3663
NML files can be imported into arbitrary datasets. Users will be asked to confirm the import process if the dataset of the NML differs from the currently active dataset. #3716

Fixed¶

Fixed a rendering bug which caused data to be clipped in certain scenarios for datasets with anisotropic resolutions. #3609
Fixed a bug where saving tracings failed after they were open for >24h. #3633
Fixed a bug that resulted in slow data loading when moving quickly through a dataset. #3656
Fixed a bug which caused the wrong magnification to be rendered when zooming out very far. #3641
Fixed a bug which broke the functionality to toggle the visibility of a tree in a skeleton tracing. #3719

19.01.0 - 2019-01-14¶

Commits

Highlights¶

You can now create tracings on datasets of other organizations, provided you have access rights to the dataset (i.e. it is public). #3533
Added the experimental feature to dynamically render isosurfaces for segmentation layers (can be enabled in the dataset settings when viewing a dataset). #3495
Added the possibility to specify a recommended user configuration in a task type. The recommended configuration will be shown to users when they trace a task with a different task type and the configuration can be accepted or declined. #3466
Added the possibility to select multiple trees in skeleton tracings in the tree tab by using ctrl + left mouse. Deleting and moving trees will affect all selected trees. #3457

Added¶

Added the possibility to select multiple trees in skeleton tracings in the tree tab by using ctrl + left mouse. Deleting and moving trees will affect all selected trees. #3457
Added the possibility to specify a recommended user configuration in a task type. The recommended configuration will be shown to users when they trace a task with a different task type and the configuration can be accepted or declined. #3466
You can now create tracings on datasets of other organizations, provided you have access rights to the dataset (i.e. it is public). #3533
Datasets imported through a datastore that is marked as 'scratch' will now show a construction-like header and error message to encourage moving the datasets to a permanent storage location. #3500
Added the experimental feature to dynamically render isosurfaces for segmentation layers (can be enabled in the dataset settings when viewing a dataset). #3495
Adds healthchecks to all Dockerfiles for automatic service healing #3606
Added possibility to load more tasks or explorative annotations in the dashboard. #3505
Adds a second colorful thumbnail for the datasets which have a segmentation layer and this segmentation thumbnail will be shown on hover over the other thumbnail. #3507

Fixed¶

Fixed a performance issue for large tracings with many branch points. #3519
Fixed bug which caused buckets to disappear randomly. #3531
Fixed a bug which broke the redirect after dataset upload via GUI. #3571

18.12.0 - 2018-11-26¶

Commits

Highlights¶

Added the possibility to add STL mesh files to tracings. #3367
Improved support for datasets with a large skew in scale. #3398
Improved performance for flight mode. #3392
Fixed the guessed bounding box for datasets that do not start at (0,0,0). #3437

Added¶

Added the possibility to add STL mesh files to tracings. #3367

Changed¶

Improved support for datasets with a large skew in scale (e.g., [600, 600, 35]). #3398
Improved performance for flight mode. #3392

Fixed¶

Fixed a bug where the initial onboarding setup failed if automatic initial data was disabled. #3421
Fixed a permission issue in the try setup.
Fixed a bug where the guessed bounding box for datasets that do not start at (0,0,0) was too large. #3437
Fixed a bug where dataset list refresh failed when datasets for non-existing organizations were reported. #3438
Editing team access rights for datasets now works even if the datastore has no disk write access. #3411
Fixed a bug where the form values when editing TaskTypes were missing. #3451
Fixed a bug which caused RGB data to not render correctly. #3455

Removed¶

Removed support to watch additional dataset directories, no longer automatically creating symbolic links to the main directory. #3416

18.11.0 - 2018-10-29¶

Commits

Highlights¶

Skeleton and volume tracings will be more unified, resulting in hybrid tracings that can contain both structures:
Hybrid tracings are now enabled by default. They allow to combine the functionality of skeleton and volume annotations in one tracing. #3399
Old volume tracing versions now also can be restored. Access it through the dropdown next to the Save button. #3349
The tracing view was improved:
The info tab in tracing views now displays the extent of the current dataset. #3371.
A User can now have multiple layouts for tracing views. #3299
More layouting improvements: #3256 #3256 #3272

Added¶

Added support for duplicate dataset names for different organizations. #3137
Extended the version restore view and added a view to restore older versions of a volume tracing. Access it through the dropdown next to the Save button. #3349
Added support to watch additional dataset directories, automatically creating symbolic links to the main directory. #3330
Added a button to the users list view that revokes admin rights from all selected users. #3378
Hybrid tracings are now enabled by default. They allow to combine the functionality of skeleton and volume annotations in one tracing. #3399
A User can now have multiple layouts for tracing views. #3299
Added support for datasets with sparse resolutions (e.g., [[1, 1, 1], [16, 16, 16]]). #3406
The info tab in tracing views now displays the extent of the current dataset. #3371.

Changed¶

The UI for editing experience domains of users was improved. #3254
The tracing layout was changed to be more compact. #3256
It is no longer possible to draw outside of a viewport with the brush tool in volume tracing. #3283
There is now a separate tracingstore module, the datastore is no longer responsible for saving tracings. #3281
The version history view shows versions grouped by day and time now. #3365
Users can now access the annotations of other users (of the same organization) given the link, even if they are non-public. #3348

Fixed¶

Fixed a layouting issue which occurred on a fresh page load when the layout was scaled to be bigger than the available space. #3256
Fixed overlap in comment tab for long tree names or comments. #3272
Fixed that CTRL + Shift + F opens two search popovers in the tracing view. Instead, the shortcut will only open the tree search now. #3407
Fixed a bug which caused data to not be displayed correctly if adjacent data does not exist.#3270
Fixed a bug which caused data to not be displayed correctly if adjacent data does not exist. #3270
Fixed a bug which caused initial rendering to sometimes miss some buckets. #3262
Fixed a bug which caused the save-button to never show success for volume tracings. #3267
Fixed a rendering bug which caused data to turn black sometimes when moving around. #3409

18.10.0 - 2018-09-22¶

Commits

Highlights¶

WebKnossos is documented now! Check it out: https://docs.webknossos.org #3011
There are multiple improvements of the tracing view:
Added customizable layouting to the tracing view. #3070
Improved general performance of the tracing view by leveraging web workers. #3162
Added a view to restore any older version of a skeleton tracing. Access it through the dropdown next to the Save button. #3194
And more usability improvements: #3126, #3066
Project administration got some UI improvements: #3077, #3224, #3233
Improved security by enabling http security headers. #3084

Added¶

Added URLs to the tabs in the dashboard. #3183
Improved security by enabling http security headers. #3084
Added the possibility to write markdown in the annotation description. #3081
Added a view to restore any older version of a skeleton tracing. Access it through the dropdown next to the Save button. #3194
Added customizable layouting to the tracing view. #3070
Added the brush size to the settings on the left in volume tracing. The size can now also be adjusted by using only the keyboard. #3126
Added a user documentation for webKnossos #3011
Tree groups can now be activated. This allows to rename a tree group analogous to renaming a tree. Also, toggling the visibility of a tree group can now be done by using the shortcuts "1" and "2". #3066
Added the possibility to upload multiple NML files during task creation, even if they are not in a zip archive
Added the possibility to supply a dedicated "sorting date" for datasets to change the sorting order in the gallery view, by default the creation date is used #3124
Added bar-chart visualization to project progress report. #3224
Added a button to collapse all comments. #3215
The datasets in the dashboard are now sorted according to their user-specific usage. As a result, relevant datasets should appear at the top of the list. #3206
3D Meshes can now be imported into the tracing view by uploading corresponding STL files. #3242

Changed¶

The modal used to change the experience of users by admins got a rework. #3077
During task creation, specifying an experience domain is now possible by choosing from existing domains. #3233
Unified the search functionality within webKnossos to implement an AND logic everyhwere. #3228
Renamed "Soma Clicking" to "Single-Node-Tree Mode". #3141
The fallback segmentation layer attribute of volume tracings is now persisted to NML/ZIP files. Upon re-upload, only volume tracings with this attribute will show a fallback layer. Use tools/volumeAddFallbackLayer.py to add this attribute to existing volume tracings. #3088
When splitting a tree, the split part that contains the initial node will now keep the original tree name and id. #3145
Improve error messages for parsing faulty NMLs. #3227
Finished tasks will be displayed with less details and sorted by their finishing date in the dashboard. #3202
Improved layouting for narrow screens. #3226
The welcome header will now also show on the default page if there are no existing organisations. #3133
Simplified the sharing of tracings. Users can simply copy the active URL from the browser's URL bar to share a tracing (assuming the tracing is public). #3176
Improved general performance of the tracing view by leveraging web workers. #3162
Improved overall drag-and-drop behavior by preventing the browser from opening the dragged file when the actual drag target was missed. #3222
The checkboxes in the user list view will clear now after the experience domains of users have been changed. #3178
Resetting a user's task requires a confirmation now. #3181

Fixed¶

Fixed a bug where large volume downloads contained invalid data.zip archives. #3086
Fixed the sorting of the dashboard task list and explorative annotation list. #3153
Fixed a missing notification when a task annotation was reset. #3207
Fixed a bug where non-privileged users were wrongly allowed to pause/unpause projects. #3097
Fixed a bug in copy-segmentation-slice feature. #3245
Fixed a regression bug which caused the initial data loading to fail sometimes. #3149
Fixed a bug which caused a blank screen sometimes when the user is not logged in. #3167
Fixed a bug where NML downloads of Task Annotations failed. #3166
Fixed a bug where viewing Compound Annotations (such as all tasks for a project in one view) failed. #3174

Removed¶

Removed the automatic redirect to the onboarding page from the default page if there are no existing organisations. #3133

18.09.0 - 2018-08-20¶

Commits

Highlights¶

The dashboard gallery loads faster #3036 and tracings in the dashboard can show their descriptions #3035.
Managing new users got easier through "new inactive users" notifications #2994, and also team managers can activate them now #3050.
Improved the UI for sharing datasets and tracings #3029.
The tracing view got a progress-indicator #2935 and scale-bars #3049.
When merging datasets within a tracing via the merge-modal, the user can choose whether the merge should be executed directly in the currently opened tracing. Alternatively, a new annotation can be created which is accessible via the dashboard, as before #2935.

Added¶

Added two new properties to mapping json files. The colors: [<hsvHueValue1>, <hsvHueValue2>, ...] property can be used to specify up to 256 custom colors for the first 256 equivalence classes of the mapping. The hideUnmappedIds: <true|false> property indicates whether segments that were not mapped should be rendered transparently or not. #2965
Added a button for refreshing the dataset in the backend cache. #2975
Added the possibility to see the description of a tracing within the dashboard. #3035
Comments of tracing trees can now be cycled through by keeping n and p pressed. #3041
All dates in webknossos will be shown in the browser's timezone. On hover, a tooltip will show the date in UTC. #2916
When merging datasets within a tracing via the merge-modal, the user can choose whether the merge should be executed directly in the currently opened tracing. Alternatively, a new annotation can be created which is accessible via the dashboard (as it has been before).
Added shortcuts for moving along the current tracing direction in orthogonal mode. Pressing 'e' (and 'r' for the reverse direction) will move along the "current direction", which is defined by the vector between the last two created nodes.
Added a banner to the user list to notify admins of new inactive users that need to be activated. #2994
When a lot of changes need to be persisted to the server (e.g., after importing a large NML), the save button will show a percentage-based progress indicator.
Changing tabs in a tracing view will not disable the keyboard shortcuts anymore. #3042
Added the possibility for admins to see and transfer all active tasks of a project to a single user in the project tab#2863
Added the possibility to import multiple NML files into the active tracing. This can be done by dragging and dropping the files directly into the tracing view. #2908
Added placeholders and functionality hints to (nearly) empty lists and tables in the admin views. #2969
Added the possibility to copy volume tracings to own account
During the import of multiple NML files, the user can select an option to automatically create a group per file so that the imported trees are organized in a hierarchy. #2908
Added the option to display scale bars in the viewports for orthogonal mode. #3049
Added functions to the front-end API to activate a tree and to change the color of a tree. #2997
When a new team or project is created, invalid names will be directly marked in red. #3034
Added an error message to the NML upload if the needed permissions are missing for the upload. #3051
Comments can now contain references to nodes (#<nodeid>) or positions (#(<x,y,z>)). Clicking on such a reference activates the respective node or position and centers it. #2950
Added a default text to the task view to indicate, that no users are assigned to a task. #3030

Changed¶

Added a checkbox to disable the warning when deleting a tree. An accidentally deleted tree can easily be restored using the Undo functionality. #2995
Improved the UI for sharing datasets and tracings. #3029
Team managers are now allowed to activate users (previously admin-only) #3050
Improved the loading time of datasets in the dashboard. #3036

Fixed¶

Fixed a bug where unloaded data was sometimes shown as black instead of gray. #2963
Fixed that URLs linking to a certain position in a dataset or tracing always led to the position of the active node. #2960
Fixed that setting a bounding box in view mode did not work. #3015
Fixed a bug where viewing Compound Annotations (such as viewing all instances of a task at once) failed with a permission issue. #3023
Fixed that the segmentation layer is loaded from the server even when the segmentation opacity is set to 0. #3067
Fixed a bug where the team name was not displayed in the task types view of admins. #3053

18.08.0 - 2018-07-23¶

Commits

Highlights¶

Performance improvements for the tracing views. #2709 #2724 #2821
Added onboarding flow for initial setup of WebKnossos. #2859
The dataset gallery got a redesign with mobile support. #2761
Improved the import dialog for datasets. Important fields can now be edited via form inputs instead of having to change the JSON. The JSON is still changeable when enabling an "Advanced" mode. #2881
Added possibility to share a special link to invite users to join your organization. Following that link, the sign-up form will automatically register the user for the correct organization. #2898

Added¶

Added release version to navbar #2888
Users can view datasets in a table from the dashboard. That view also allows to create explorational tracings (which had to be done via the gallery view for non-admins before). #2866
Added the task bounding box of a skeleton tracing to NML files. #2827 \ Example: <taskBoundingBox topLeftX="0" topLeftY="0" topLeftZ="0" width="512" height="512" depth="512" />
Added the possibility to kick a user out of the organization team. #2801
Added a mandatory waiting interval of 10 seconds when getting a task with a new task type. The modal containing the task description cannot be closed earlier. These ten seconds should be used to fully understand the new task type. #2793
Added possibility to share a special link to invite users to join your organization. Following that link, the sign-up form will automatically register the user for the correct organization. #2898
Added more debugging related information in case of unexpected errors. The additional information can be used when reporting the error. #2766
Added permission for team managers to create explorational tracings on datasets without allowed teams. #2758
Added higher-resolution images for dataset gallery thumbnails. #2745
Added permission for admins to get tasks from all projects in their organization. #2728
Added the shortcut to copy the currently hovered cell id (CTRL + I) to non-volume-tracings, too. #2726
Added permission for team managers to refresh datasets. #2688
Added backend-unit-test setup and a first test for NML validation. #2829
Added progress indicators to the save button for cases where the saving takes some time (e.g., when importing a large NML). #2947
Added the possibility to not sort comments by name. When clicking the sort button multiple times, sorting is switched to sort by IDs. #2915
Added displayName for organizations. #2869
Added onboarding flow for initial setup of WebKnossos. #2859
Added the possibility to show the task in a random order. #2860

Changed¶

Improved the search functionality in the datasets view. The datasets will be sorted so that the best match is shown first. If a different sorting is desired, the sorting-arrows in the columns can still be used to change the sorting criteria. #2834
Improved performance in orthogonal mode. #2821
When deleting the last node of a tree, that tree will not be removed automatically anymore. Instead, the tree will just be empty. To remove that active tree, the "delete" shortcut can be used again. #2806
Renamed "Cancel" to "Reset and Cancel" for tasks. #2910
Changed the type of the initial node of new tasks to be a branchpoint (if not created via NML). #2799
The dataset gallery got a redesign with mobile support. #2761
Improved the performance of saving large changes to a tracing (e.g., when importing a large NML). #2947
Improved loading speed of buckets. #2724
Changed the task search, when filtered by user, to show all instead of just active tasks (except for canceled tasks). #2774
Improved the import dialog for datasets. Important fields can now be edited via form inputs instead of having to change the JSON. The JSON is still changeable when enabling an "Advanced" mode. #2881
Hid old paused projects in the project progress report even if they have open instances. #2768
Excluded canceled tasks and base tracings from the list at api/projects/:name/usersWithOpenTasks. #2765
Streamlined the order in which initial buckets are loaded when viewing a dataset. #2749
Reduced the number of scenarios in which segmentation-related warnings are shown (e.g, not for skeleton tracings when there are multiple resolutions for segmentations anyway). #2715
Email addresses for notifications about new users and about task overtime are no longer specified instance-wide but once per organization. #2939
Improved tracing view page load performance by decreasing WebGL shader compilation time. #2709
Improved error reporting for project progress page. #2955
Redesigned the user task list to make it easier to read the whole task description. #2861

Fixed¶

Fixed a bug which caused segmentation data to be requested as four-bit when four-bit-mode was enabled. #2828
Fixed a bug where possible comments or branchpoints sometimes were not properly deleted when deleting a node. 2897
Fixed a bug which caused projects to be unpaused when the project priority was changed. #2795
Fixed an unnecessary warning when deleting a tree in a task, that warned about deleting the initial node although the initial node was not contained in the deleted tree. #2812
Fixed a bug where the comment tab was scrolled into view horizontally if a node with a comment was activated. #2805
Fixed a bug in for Firefox users where a long tree list created an unnecessary scroll region. #2787
Fixed clicking on a task type within the task list page, so that the task type page will actually only show the linked task type. #2769
Fixed clicking on a project within the task list page, so that the project page will actually only show the linked project. #2759
Fixed a bug in the front-end API's setMapping call which caused ignored calls if the provided object was mutated. #2921
Fixed a bug where cell IDs in the segmentation tab were not shown for all zoomsteps. #2726
Fixed the naming of the initial tree in tasks. #2689
Fixed a regression affecting node selection, shortcuts and 3d viewport navigation. #2673
Fixed the dataset zip upload for datasets, which only have one data layer and no config file. #2840
Fixed a bug where task deletion broke the task listing for users who had active annotations for the task #2884
Fixed that decimal scales (e.g., 11.24, 11.24, 30) couldn't be defined for datasets in "simple" mode. #2912

18.07.0 - 2018-07-05¶

First release