Speckle Position and Velocity Calculations 

JFilament
Speckle TrackerJ
Leading Edge Position and Velocity
Leading Edge Intensity
Correlation Analysis
Speckle Velocities

The plugin Speckle_Velocity calculates the velocity of retrograde flow from tracks of speckle position generated in
Speckle TrackerJ. It also requires a snake file generated in JFilament to indicate the position of the cell's leading edge and the output of LE_Velocity. When Speckle_Velocity is run it will prompt the user to input parameters:


The user will then be prompted to select 3 data files:
  1. A velocity matrix (the output of LE_Velocity)
  2. A snake file (the output of JFilament)
  3. A speckle file (the ouput of Speckle TrackerJ)

Output data file: Contains the calculated speckle velocity data in two formats. The first,
a duplicate stack displaying vector flow maps of speckle velocities. A value of S=1 yields velocity vectors that scale 1nm/s per pixel. The second is a data file formatted: speckle number, frame  number, speckle lifetime (s), angle (degrees), distance from the leading edge (Ám), local leading edge speed (nm/s), net speckle speed (nm/s), x-component of the speckle velocity (nm/s), y-component of the speckle velocity (nm/s).

A second plugin, Speckle_Velocity_NoSnakes, calculates speckle velocities as a function of time and lifetime.
When Speckle_Velocity_NoSnakes is run it will prompt the user to input parameters:
The user will then be prompted to select a speckle file.

Output data file: Contains the calculated speckle velocity data in two formats. The first, a duplicate stack displaying vector flow maps of speckle velocities. A value of S=1 yields velocity vectors that scale 1nm/s per pixel. The second is a data file formatted: speckle number, frame  number, speckle lifetime (s), net speckle speed (nm/s), x-component of the speckle velocity (nm/s), y-component of the speckle velocity (nm/s).

References:

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