Add further features for spots and branch graph

[stefanhahmann]

User Story

A user may want to have additional features on the branch graph for some analysis.

Further Features requests

• https://docs.google.com/document/d/107yOWeroBS3xZWMTV1Ieuv8u0m1KO-eA3JgH7qhA5_s/edit

Possible Features

Spot Features:

• Axes lenghts, i.e. minor axis, middle axis, major axis. The axes should be derivable from this, cf. Spot#getCovariance.
• Spot volume, spot radius already exists. The ellipsoids are shown in BigDataViewer. The axes should be derivable from this, cf. SpotRadiusFeature. SpotEllipsoidFeature #13
• aspect ratios of ellipsoid axes
  • 3 ratios considering 2 axes each SpotEllipsoidAspectRatiosFeature #15
  • further ratios considering all 3 axes, e.g. (b-c)/(a-c). a .. major axis, b .. middle axis, c .. minor axis
• Descriptors of the cell in relationship to its neighbours
  • Average distance to 5(?) nearest - neighbours Average distance to n nearest neighbours #6
  • Further descriptors available in CLIJ
• Texture params, i.e. histogram analysis within spot - how to express with a few numbers??? E.g. mean, median, variance of grey values. Perhaps frequency based indicators.
• Division orientations (a 3 dimensional vector)
• Time-resolved lineage data
  • Moving average of intensity (e.g. average including the previous 3 and the next 3 spots)
• Link between Spots and BranchSpots Add computer for BranchSpot id  #37

BranchSpot Features:

• Movement:
  • Movement speed Movement speed BranchSpot Feature #61
  • Movement directionality Movement directionality #62
  • Movement relative to neighbours Movement (speed and directionality) relative to neighbours  #65
• Average velocity / Movement speed. May be derived from displacement and duration. It needs to be checked, if displacement equals the distance along the cell path.
• Measure for how direct the movement of the cell ("directness of movement") is, i.e. "distance along cell path" / "euclidean distance between cell divisions" (cf. https://en.wikipedia.org/wiki/Sinuosity)
  • Sinuosity of cell during life cycle #11
• Cell behaviour:
  • Growing cell / shrinking cell
    • Volume quotient between cell divisions
    • Average growth/shrinking rate
    • Absolute delta of growth/shrinking
• Average spot intensities
• Generation:
  • Time since last division
    • not resolvable at the moment due to non-existing time units in BDV
    • cf. also discussion here: Generation time of a BranchSpot #7
    • difference of TimePoints is available instead
    • Two implementations:
      • "Branch duration: https://github.com/mastodon-sc/mastodon/blob/master/src/main/java/org/mastodon/mamut/feature/branch/BranchDisplacementDurationFeature.java
      • "Branch N spots": https://github.com/mastodon-sc/mastodon/blob/master/src/main/java/org/mastodon/mamut/feature/branch/BranchNSpotsFeatureComputer.java
  • Generation number
    • already implemented as "Branch depth"
    • https://github.com/mastodon-sc/mastodon/blob/master/src/main/java/org/mastodon/mamut/feature/branch/BranchDepthFeatureComputer.java
    • Speed of cell division Speed of cell division #63
    • Normalized number of cell divisions in track Normalised number of cell divisions in track #64
• Topology descriptors:
  • Number of divisions of a BranchSpot
    • Implemented as "Branch N divisions"
    • Usually 2 or 0 (the latter one in case of a leave in the lineage tree)
    • https://github.com/mastodon-sc/mastodon/blob/master/src/main/java/org/mastodon/mamut/feature/branch/BranchNDivisionsFeature.java
  • Number of total leaves of a BranchSpot (until a certain timepoint)
    • Number of total leaves of a BranchSpot #9
  • Number of BranchSpot successors of a BranchSpot
    • Number of total leaves of a BranchSpot #9 $number\ of\ BranchSpot\ successors\ of\ a\ BranchSpot = 2 * number\ of\ total\ leaves - 2$

BranchLink Features:

• Type of Division (symmetric/asymmetric)
  • Proportion of size/volume compared to the "sister"-cell (i.e. the other "daughter"-cell of the cell division)
• Orientation of Division for both "daughter"-cells (i.e. BranchLinks)

Discussion:

• Which features may be useful?
• Are there further features?

• Extend Grapher with Branch Features?

Overall Goal:

• Identify important params that may predict cell life fate