TrackMate Workflow

[Rory235]

Hi There

I am brand new to Knime and I am not to sure what I am doing. I am using the Image processing suite for ImageJs track mate. I have used Trackmate on its own in ImageJ successfully but I need to get more information out of it and found out about Knime through a forum post. I have found a few workflows online but they don’t seem to work and I am definatley fumbling around when I try and do it my self.

Could some one point me in the direction of a tutorial or successful workflow

[Rory235]

Hi there

I am new to knime and I am trying to use Trackmate to track some particles. The workfloiws I found online dont work anymore (I’m guessing this is due to software updates). I keep getting this error on the TrackMate node and dont know whats causing it or how to fix it. I am guessing one of the outputs from the spot detection module isnt what the trackmate module is needs? Any help would be aprreciated!

[thor_landstrom]

Hello @Rory235,

I found one on the hub that works for me out of the box (although the joiner is deprecated, it should still run and it is an easy fix to replace with the new one)

Application: Trackmate – knime

This should have some reference material for you to work off of to see how to run it.

Hope this helps,
TL

[Rory235]

Hi there

Thats what I was using before and what gave me the errors.

Thanks for the help either way though!

[thor_landstrom]

That is weird, it works on my end. Are you passing a table input with the column of ‘Labeling’ type?

I did a quick test and it will output the error you are getting if you do not have a column of that type.

For the workflow I attached earlier, that is just the column called ‘Source Labeling’ of type ‘Labeling’

Try to make sure you pass in the column with the ‘Labeling’ type to see if the error goes away.

TL

[Rory235]

Not going to lie, I have no idea how to do that, I have never used knime before. Dont worry about it though. I have managed to export the .csv from trackmate using it as a stand alone software (literally just figured it out) but that you very much for trying