Problems retrieving intensity measurement with TrackMate CSV Importer

Hi Everyone!

I’ve tracked my files using Manual Tracking in FIJI, and want to reimport those xyt-track coordinates into TrackMate to extract mean intensity data for a radius around the xy coordinate in multiple channels. However, using the TrackMate CSV Importer tool, I’m not getting any intensity values (the display options shows 0.0 to 0.0, spot statistics all 0) for mean, min, max intensity. It looks like it has all of the other data, xy coordinates, time/frame, track index, and Trackmate is calculating velocity fine, just no intensity measurements. Any idea what I should do? Thanks for your help!

EDIT: I installed the TrackMate Extras, and now It shows me zeros for intensity in 10 channels :slight_smile:


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Hi Sara, Are you able to share any of the relevant files with us?

Sure! It’s a large TIF though, here is a Google Drive link to an example CSV and TIF timelapse . Thanks for checking it out!

Bumping because I have not had time to check it out. Obviously, the CSV file does not contain intensity info.

I wonder if the coordinates need to be translated into ImageJ ROIs first and then measured.

The csv file contains the tracks and xyt coordinates that I am importing using the TrackMate CSV Importer, with the goal of calculating spot statistics in TrackMate to retrieve intensity values from those coordinates (for a given spot radius) at each time point and for each track. The importer works, it calculates the velocity of each spot, but it does not calculate the intensity values of those imported ROIs.

@markkitt If there is another way, besides TrackMate, to load XYT data, dilate that multipoint selection to ROIs of a defined radius, and measure the intensity on the correct slice, that’d be great too, but I don’t know of anything able to do slice specific measurements besides TrackMate.

@tinevez I wonder if you might have any ideas about my issue with TrackMate CSV Importer? Again, uploading the CSV file with Compute All Features checked, and there are no Mean Intensity Values given for any of the channels. Thanks in advance for your thoughts!

Hello @sparkerino

I checked your data and actually I think it is related to a problem with spatial coordinate units.

TrackMate expects the spot position in the CSV file to be in the same units that in the image. In your image, the units is µm, but in the CSV file it looks like it is pixels.

So the spots get created at an incorrect position (in my tests, out of the image) which yields the bug you see.

My recommendation would be to recompute the X and Y position in the CSV file in µm, by simply multiplying them by the pixel size.

Tell us if it works

Totally forgot to remove the scale on the file (or scale the coordinates)! So it’s measuring all the spots in the corner again, huh? And you were right, it’s giving intensity measurements now. Thank you very much for taking a moment to help me out :slight_smile:

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