trackmate-sc
Add option to export tracks overlayed on max-z projection for 3D time series data
Posting this here based on my question on image.sc. This seems like it could be a useful enhancement, but I don't know how much interest there would be in such an option.
I have a time series of 3D images with particles that I have localized using TrackMate. Now I would like to export the overlayed tracks and display them over the max-z projection of the images. However, with TrackMate it seems like my only option using the “Capture Overlay” action is to export a single z-plane with the overlays.
Desired behavior: In the "Capture Overlay" dialog include a check box or drop-down menu to select doing a no projection, a max-z projection, or potentially a projection along another axis before capturing the results
Current workaround: So far the only solution I am aware of is to save the TrackMate settings in an XML file using the save dialog, then copy the XML file and replace the references to the original TIF file with references to a new TIF file which is the max-z projection of the original data. Then when I load this TIF file with Plugins → Tracking → Load a TrackMate File the max-z projection image is loaded and I can use the TrackMate “capture overlay” action to get the image that I wanted.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/export-trackmate-tracks-on-max-z-projection-for-3d-time-series-data/64487/4
Presumably this can be achieved by editing a few lines in CaptureOverlayAction.java ... easier said than done I'm sure