Export¶

Label Image Export¶

Menu Location: File > Export > Export label image using ellipsoids
The Label image exporter is capable of saving a label image to a file using the existing ellipsoids in Mastodon.
For the labels, the spot ids, branch spot ids or the track ids that correspond to the spots / ellipsoids may be used. Since these Ids are counted zero based in Mastodon, an offset of 1 is added to all Ids so that no label clashes with the background of zero.
The recommended export format is ‘*.tif’-files. However, it should work also for other formats supported by ImageJ.
The export uses an image with signed integer value space, thus the maximum allowed id is 2.147.483.646.
The dialog:

Label Id: The id that is used for the labels. The default is the Spot track Id.
- The ids correspond to the highlighted columns in the feature table:
Frame rate reduction: Only export every n-th frame. 1 means no reduction. Value must be >= 1.
- The frame number corresponds to the Spot frame column in the feature table.
Resolution level: Spatial resolution level of export. 0 means highest resolution. Value > 0 mean lower resolution.
Save to: Path to the file to save the label image to. Should end with ‘.tif’.

Menu Location: File > Export > Export to GraphML (branches)
Exports the branch graph to a GraphML file.
- The graph is directed. The branch spots are the vertices and the branch links are the edges.
- The vertices receive a label attribute with the branch spot name. The vertices receive a duration attribute with the branch duration.
- The edges are not labeled and have no attributes.
GraphML can be visualized with Cytoscape, yEd or Gephi.
GraphML can be processed in Java using the JGraphT library.
GraphML can be processed in Python using the NetworkX library.

Export all branches to GraphML (one file)
- Exports the whole branch graph to a single file.
- Select a file to save to. Should end with ‘.graphml’.
Export selected branches to GraphML (one file)
- Exports the selected branches to a single file.
  - The selected branches are the ones that are highlighted in the branch view.
  - A branch is considered selected if at least one of its spots is selected. However, the exported duration attribute always reflects the whole branch duration.
- Select a file to save to. Should end with ‘.graphml’.
Export tracks to GraphML (one file per track)
- Exports each track to a separate file.
- Select a directory to save to.