Mastodon Deep-Lineage

What's Changed

• Add Median line to lineage classification dendrogram by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/60

• Add Movement speed feature by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/66

• Add Movement direction feature by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/67

• Add Predecessors count feature by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/68

• Add Normalized cell divisions feature by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/69

• Add Movement relative to neighbours feature (spot and branch level) by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/74

• Add Branch Graph export to Graphml by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/76

  • 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.
  • Options
    • Export all branches to GraphML (one file)
    • Exports the selected branches to a single file.
    • Select a file to save to. Should end with '.graphml'.
  • Example
    • Demo data: Example data set
    • The resulting file loaded into yEd:
    • The resulting file loaded into Cytoscape:

• Add Plugin to Import spots from label images by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/79 positions of each label.

  • You can use the plugin to import spots from a label image representing an instance segmentation into Mastodon. This may be useful if you have an instance segmentation of cells or other objects, and you want to track them using Mastodon.
  • The label image is expected to contain the spot ids as pixel values.
  • The label image is expected to have the same dimensions as the image data in Mastodon.
  • Labels are processed frame by frame.
  • Multiple blobs with the same id in the same frame are considered to belong to the same spot by this importer. It is advised to use a unique ids for spots in the same frame.
  • The resulting spots are ellipsoids with the semi axes computed from the variance covariance matrix of this pixel
  • The resulting spots may be linked using the linker plugin in Mastodon (Plugins > Tracking > Linking...) or Elephant.
  • Parameters linked.
    • Ellipsoid scaling factor: The scaling factor to apply to the ellipsoids. The default is 1.0. The scaling factor is applied to the semi axes of the ellipsoids. The ellipsoid scaling factor can be used to increase (>1) or decrease ( <1) the size of the resulting ellipsoid. 1 is equivalent of ellipsoids drawn at 2.2σ.
    • Link spots having the same id in consecutive frames: If checked, spots with the same id in consecutive frames are
  • Example:

• Add Conversion script for ASTEC data to mastodon (only demo code, not in production) by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/70

• Fix bug in some lineage classification scenarios by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/77

Full Changelog: https://github.com/mastodon-sc/mastodon-deep-lineage/compare/mastodon-deep-lineage-0.0.1...mastodon-deep-lineage-0.1.0