Comments (5)
We've been using TrackMate from within KNIME successfully with these plugins:
https://github.com/fmi-faim/fmi-ij2-plugins/
Having the track data in KNIME makes MSD analysis really easy. For a use case (in this case relative MSD between paired tracks of two channels), see this paper and the attached workflow: http://doi.org/10.13140/RG.2.2.16490.31688
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Hi @howlermonkeys
Most likely not in the Mastodon directly. You would export tracks in an data analysis software and perform MSD fitting there. Example http://tinevez.github.io/msdanalyzer/
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Just to make sure: we're talking about TrackMate and not TrackMate3 (i.e. this repository, aka Mastodon) currently, right?
In TrackMate, I see Velocity being reported for each link between to vertices, and Mean track speed for each track. I see no problem in reporting a velocity for each frame-to-frame link, but of course it should not be confused with a per-track speed. Isn't the reporting clear enough?
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Related Issues (20)
- Mastodon Exceptions Occurred During Plugin Discovery HOT 1
- Add timepoint and number of spots info to BDV View HOT 1
- Saving and Reloading BranchSpot Feature in Table does not work HOT 1
- Compute features option not working in Mastodon HOT 6
- BDV Brightness Settings dialog cannot be opened anymore HOT 9
- Tags are not shown in Edit Window of Data Table HOT 1
- Remove KeyMap binding for Brightness dialog
- bugs in Mastodon launcher HOT 2
- displaying bug in TrackScheme HOT 1
- project with .xml pointing on TIFF series is not opening HOT 5
- Adding new spots fails after deleting all spots HOT 11
- Mastodon may freeze with overlay visibility track of focused vertex HOT 7
- Backup of Mastodon files HOT 4
- Expected behaviour of Bdv Branch View HOT 2
- Show Branch Feature in TrackScheme and Bdv
- Provide textual way to search and run commands in Mastodon HOT 13
- Increase File integrity during file saving HOT 3
- Make font size of TrackScheme adjustable
- Selection Table for BranchSpots and BranchLinks
- Show Spot Id in TrackScheme based on User settings
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