The goal of tracing skeletons is to reconstruct structures in a dataset that span across many data slices as a graph of connected nodes. A typical example of a skeleton annotation is to follow a nerve cell for a few nanometers, placing a node every few slices. (See image below)
A typical skeleton annotation contains the reconstruction of one or more structures, often with many thousand nodes. All connected nodes form a tree or more generally speaking a graph.
Skeleton annotations can be downloaded, modified, imported using a human-readable XML-based file format called NML.
This article outlines commonly used features and operations for viewing, editing, or creating new skeleton annotations in webKnossos.
webKnossos supports several modes for displaying your dataset & interacting with skeleton annotations.
Orthogonal mode displays a dataset with the camera oriented orthogonally to each of the three main axis x, y, z. Additionally, a fourth viewport shows the data and skeletons from a 3D perspective. All camera movements happen along the respective main axis. This view is especially useful for viewing your data in the highest possible quality alongside its main imaging axis, typically XY. Every single slice of the raw data can be viewed.
Most skeleton tracing operations and keyboard shortcuts are tailored for the Orthogonal Mode.
Oblique mode presents an arbitrarily-resliced view through the data. In contrast to Orthogonal mode, any arbitrary slice through the dataset at any rotational angle of the camera is possible.
Flight mode also allows a resliced view through the data. In contrast to Oblique mode, the data is projected on the inside of a sphere with the camera located at the center of the sphere.
Spherical projection is especially useful when rotating the camera, as pixels close to the center of the screen move in a predictable manner. Interactions and movements in Flight mode feel similar to First-Person-View (FPV) games.
Flight mode is best used for annotating structures very quickly. Trained tracers can follow "tube"-like structures as though they are "flying" through them. Nodes are placed automatically along the flight path, creating skeleton very efficiently.
Skeleton annotations consist of connected nodes forming a graph. Nodes are connected through edges and are organized in trees.
Nodes can be placed by right-clicking (Right Click) in orthogonal mode or automatically when moving in flight or oblique mode. webKnossos uses the concept of always having an active node and an active tree. All (global) operations are executed on the current active node, e.g. adding a comment or node deletion. Most keyboard shortcuts take the active node into context. Operations on whole trees, e.g. splitting or merging trees, follow the same pattern.
Skeleton annotations can contain one or many trees consisting of several nodes all the way to millions of nodes. Users can add comments to each node to mark important positions or easily select them from a list of comments for later usage. Comments are organized in the
Comments tab on the right-hand side of the screen. The
Tree Viewer tab on the right-hand side menu displays a 2D simplified tree representation of the currently active tree.
Many organic structures do not follow a single, linear path but split into several individual branches instead. webKnossos natively supports branch points. Any node can be marked as a branch point using the keyboard shortcut "B". Branch points are highlighted using a slightly different color. All branch points are saved as a stack for each tree and can be accessed first-in, first-out (FIFO). Press the "J" to jump to the latest branch point to continue working from there and remove it from the stack.
Create New Node
SHIFT + Left Click
Select Node (Mark as Active Node)
Center Camera on Active Node
Delete Active Node
Create Branch Point
Jump to Last Branch Point
Create New Tree
All further keyboard shortcuts are available here.
All operations and information regarding trees are organized under a tab called
Trees on the right-hand side of the screen.
A typical skeleton annotation consists of one or more trees. Trees can be nested and organized in so-called
Tree Groups. Tree groups can have a name and are used to structure and label your annotation even further. Trees can be dragged and dropped between tree groups. This action can be applied to multiple trees by selecting them with Ctrl + Left Mouse (on Mac OS Cmd + Left Mouse). Hover over existing tree groups to bring up a little menu for creating new groups and deletion. It also has options to expand and collapse all subgroups. Renaming of a group can be done by selecting a group and then entering the new name into the input above the tree hierarchy structure view.
Common tree operations include splitting and merging trees.
Tree splitting can be done in two ways:
Select a node at which to split (SHIFT + Left Click) and delete (DEL) it.
Delete an edge between two nodes. Select the first node (SHIFT + Left Click), then SHIFT + CTRL + Left Click on the second node of the edge to delete this connection.
Tree merging works similarly to edge deletion but will create a new edge between two previously unconnected trees. Select the first node and SHIFT + ALT + Left Click the second node to create an edge between the two.
A random color is assigned to each tree upon creation. Colors can be shuffled for a single tree or for all trees in a skeleton. Use the overflow menu under
More in the tree tab and select
Change Color or
Shuffle All Colors to assign new randomly chosen colors. All node have the same color as their parent tree and can not be changed individually. The active node, branch points, and node that have comments assigned to them are highlighted with a slight variation of the tree's color.
The visibility of individual trees can be toggled to hide some trees for a better overview. Toggle the checkbox before each tree name or tree group to hide/show it. Alternatively, the visibility of all trees can be toggled all at once using the
Toggle All /
Toggle Inactive button under the
Tree Tab. There are also keyboard shortcuts to quickly toggle the visibility:
Toggle Visibility of all Trees
Toggle Visibility of Inactive Trees
SHIFT + ALT + Left Click
Merge Two Nodes and Combine Trees
SHIFT + CTRL + Left Click
Delete Edge / Split Trees
webKnossos makes it easy to import or export skeleton annotations as NML files. There are two ways for downloading your annotations:
There is a
Download button in the overflow menu next to the prominent
Save button in the toolbar at the top of the screen.
If you need more fine-grained control over which trees to download use the
Download Selected Trees option. From the
Trees Tab click on
More and select
Download Selected Trees from the menu. All visible trees (checkmark in front of the name) will be downloaded as an NML file. This is especially useful if you need to only download a single tree of an otherwise much larger tracing.
Importing a skeleton annotation can be achieved using two approaches as well:
If you already have an annotation open you can easily add more skeletons to it by drag and dropping an NML file onto your browser window. Otherwise, use the
Import NML option next to
Download Selected Trees. This will merge the NML file's content with the already open annotation.
To import a skeleton annotation as a completely new webKnossos annotation, just drag and drop the NML file anywhere on your user dashboard. Alternately, navigate to your user dashboard and use the
Upload Annotation button within the "Explorative Annotations" section.
There are two ways for merging annotations:
While in the tracing UI, drag and drop an NML file onto your browser window to import a skeleton. The imported skeleton will be merged with currently open annotation.
If you would like to merge your current annotation with another existing annotation, select the
Merge operation from the overflow menu next to the
Save button. (see image) Either enter the ID of an existing explorative annotation or select a whole project and proceed to merge the selection with your currently open annotation. The resulting annotation can either be created as a new explorative annotation. Otherwise, the merge will happen in your current annotation.