mastodon-deep-lineage-0.3.4

What's Changed

• Enable Import of Spots from segmented Image data for 2D images by @stefanhahmann in #121

Full Changelog: mastodon-deep-lineage-0.3.2...mastodon-deep-lineage-0.3.4

mastodon-deep-lineage-0.3.3

Build against Mastodon core beta-32 release and with pom-scijava 39.0.0

Full Changelog: mastodon-deep-lineage-0.3.2...mastodon-deep-lineage-0.3.3

mastodon-deep-lineage-0.3.2

This release has been built against the API of Mastodon-Beta-31.

• Changed the menu location of the export, import, feature computation and lineage clustering function
• Fixed a small bug that occurred in the dialog of the cluster lineages command by making the external projects file list non persistent

Full Changelog: mastodon-deep-lineage-0.3.0...mastodon-deep-lineage-0.3.2

mastodon-deep-lineage-0.3.0

What's Changed

• Add possibility to perform dimensionality reduction using Umap algorithm by @stefanhahmann in #113
  • This can be tested using https://github.com/mastodon-sc/mastodon-example-data/tree/master/tgmm-mini
  • 
• Hierarchical clustering of lineage trees using multiple similar projects by @stefanhahmann in #107
  • This can be tested using https://github.com/mastodon-sc/mastodon-example-data/tree/master/astec
• Export result of hierarchical clustering of lineage trees to CSV by @stefanhahmann in #112
  • 
• Select resolution level in export ellipsoid to label image by @stefanhahmann in #106
• Rename function lineage classification to hierarchical clustering of lineage trees by @stefanhahmann in #115
• Update pom-scijava to version 38.0.1 by @stefanhahmann in #108

Full Changelog: mastodon-deep-lineage-0.2.1...mastodon-deep-lineage-0.3.0

mastodon-deep-lineage-0.2.1

What's Changed

• Bugfixes in Import Spots from Label Image
  • Make Import Spots handling single pixels and planar pixels properly by @stefanhahmann in #105
  • Correctly apply transformation matrices of images by @stefanhahmann in #105
  • Let the user specify the channel that has been used for external segmentation during import of spots from image by @stefanhahmann in #105

Full Changelog: mastodon-deep-lineage-0.2.0...mastodon-deep-lineage-0.2.1

Mastodon Deep-Lineage 0.2.0

What's Changed

• Improvements to Lineage Classification and Dendrogram
  • Make dendrogram panel configurable, i.e. control labeling for leaves with root cell names, show tag values and select tag set for it and allow toggling the threshold and the median line by @stefanhahmann in #98
    • This can be tested with these example datasets: https://github.com/mastodon-sc/mastodon-example-data/tree/master/astec
  • Allow the lineage classification in case the number of valid roots equals the number of classes. This allows by deriving the similarity of two lineage trees from the dendrogram. @stefanhahmann in #89
    
  • Add export of functionality (PNG and SVG) to dendrogram and make it scrollable if needed by @stefanhahmann in #88
    
  • Performance optimization of tree edit distance (~factor 10) by @stefanhahmann in #102
    • Performance tests can be made using this synthetic dataset:
      flatSim2_be_2aba_1bab.zip
    • Parameters that should work are crop start time: 30, crop end time: 350. Larger time windows may take very long time to be processed.
  • Add 2 new similiarity measures that contain normalization in the local cost function by @stefanhahmann in #90
    
  • Bug fix: take start time into account for lineage tree classification by @stefanhahmann in #104
• Unit Tests
  • Migrate all unit tests from junit 4 to junit 5 by @stefanhahmann in #95

Full Changelog: mastodon-deep-lineage-0.1.1...mastodon-deep-lineage-0.2.0

Mastodon Deep-Lineage 0.1.1

What's Changed

• Add Median line to lineage classification dendrogram by @stefanhahmann in #60
  

• Add Movement speed feature by @stefanhahmann in #66

• Add Movement direction feature by @stefanhahmann in #67

• Add Predecessors count feature by @stefanhahmann in #68

• Add Cell cell division frequency feature by @stefanhahmann in #69

• Add Movement relative to neighbours feature (spot and branch level) by @stefanhahmann in #74

• Add Branch Graph export to Graphml by @stefanhahmann in #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 #79

  • 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
    positions of each label.
  • The resulting spots may be linked using the linker plugin in Mastodon (Plugins > Tracking > Linking...)
    or Elephant.
  • Parameters
    • 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
      linked.
  • Example:
    

• Add Conversion script for ASTEC data to mastodon (only demo code, not in production) by @stefanhahmann in #70

• Fix bug in some lineage classification scenarios by @stefanhahmann in #77

Full Changelog: mastodon-deep-lineage-0.0.1...mastodon-deep-lineage-0.1.0

Mastodon Deep-Lineage 0.0.1

Contents of Mastodon Deep-Lineage 0.0.1

Numerical Features added to Mastodon

• Spot Features

  • Spot Ellipsoid Axes and Volume
  • Spot Ellipsoid Aspect Ratios
  • Spot Branch ID

• Branch-spot Features

  • Branch N Leaves
  • Branch N Successors
  • Branch Sinuosity

Lineage Tree Classification

• Grouping similar lineage trees together.
  • The lineage classification dialog
  • The resulting dendrogram
    
  • The resulting tag set used for coloring the track scheme.
    
  • More documentation:

Label image exporter

• Saving a label image to a file using the existing ellipsoids in Mastodon.
• The dialog:
• The timelapse with the ellipsoids in BigDataViewer:
• The exported tif imported into Napari 3D view:

Contributors

• @stefanhahmann
• @maarzt
• @tinevez

What's Changed

• Number of total leaves of a BranchSpot by @stefanhahmann in #10
• Add new Feature BranchSinuosity by @stefanhahmann in #18
• Add logback as logging framework by @stefanhahmann in #19
• Add SpotEllipsoidFeature by @stefanhahmann in #14
• Add SpotEllipsoidAspectRatioFeature by @stefanhahmann in #23
• Add Zhang Tree Edit Distance for labeled unordered trees by @stefanhahmann in #26
• Add Branch spot id feature by @stefanhahmann in #39
• Extend the ZhangUnorderedTreeEditDistance to Return the Optimal Node Mapping by @maarzt in #33
• Classification of lineage trees by @stefanhahmann in #32
• Add exporting ellipsoids to file by @stefanhahmann in #45
• Colorize dendrogram by @stefanhahmann in #48
• Add Readme.md by @stefanhahmann in #57

New Contributors

• @maarzt made their first contribution in #31

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