Import Through UI

Uploading through the web UI¶

The easiest way to get started with working on your datasets is through the WEBKNOSSOS web interface. You can directly upload your dataset through the browser.

From the Datasets tab in the user dashboard, click the Add Dataset button.
Drag and drop your data (a folder, a zip archive or image files) into the upload section, or use Choose folder / Choose files. WEBKNOSSOS recognizes the format of your data from its file names and tells you whether it is ready to view or will be converted after the upload. Click How should my folder look? to see the expected folder structure for each format.
Check the dataset details, which are filled in automatically:
- the name (proposed from the folder, archive or file names)
- the target folder
- additional teams that should have access to the dataset
- the voxel size and its unit (e.g., nanometers), only if your data needs to be converted
Click the Upload button

Internally, WEBKNOSSOS uses the Zarr3 format by default to display your data. If your data is already in a data format like WKW, Zarr or Zarr3 you can simply drag your folder (or zip archive of that folder) into the upload view.

If your data is not in WKW or Zarr format, you can either:

upload the data in a supported file format and WEBKNOSSOS will automatically import or convert it (webknossos.org only). Depending on the size of the dataset, the conversion will take some time. You can check the progress at the Jobs page or the "Datasets" tab in the dashboard. WEBKNOSSOS will also send you an email notification.
Convert your data manually to WKW. For this, we provide the following software tools and libraries:
- The WEBKNOSSOS CLI is a CLI tool that can convert many formats to WKW.
- For other file formats, the WEBKNOSSOS Python library can be an option for custom scripting.

In particular, the following file formats are supported for uploading (and conversion):

WKW dataset
OME-Zarr datasets
Image file sequence in one folder (TIFF, JPEG, PNG, DM3, DM4)
Multi Layer file sequence containing multiple folders with image sequences that are interpreted as separate layers
Single-file images (OME-Tiff, TIFF, PNG, czi, raw, etc)
Neuroglancer Precomputed datasets
N5 datasets

We support a variety of data types for the uploaded data. To make sure that your data can be uploaded to WEBKNOSSOS take a look into this table of supported data types for color and segmentation layers:

dtype	Color Layers	Segmentation Layers
uint8	✓	✓
uint16	✓	✓
uint24 rgb	✓	does not apply
uint32	✓	✓
uint64	✗	✓

int8	✓	✓ (ids should¹ still be positive)
int16	✓	✓ (ids should¹ still be positive)
int32	✓	✓ (ids should¹ still be positive)
int64	✗	✓ (ids should¹ still be positive)

float	✓	✗
double	✗	✗

¹ While rendering of negative segment IDs is supported currently, interaction with segments (including annotating them) is only supported for positive IDs.

Once the data is uploaded (and potentially converted), you can further configure a dataset's Settings and double-check layer properties, fine tune access rights & permissions, or set default values for rendering.