Ilastik csv output column names in tracking workflow

I have a csv output from Ilastik with the column names:

  • frame
  • labelimageId
  • trackId
  • lineageId
  • parentTrackId
  • mergerLabelId

We are trying to construct a lineage based on the time of division and for how long it lived by connecting parent cell division to daughter cell creation. Can you elaborate on what each column describes and how the numbers in the columns relate to other columns?

Thank you!

Hello @Shakthi_Visagan

  • frame: time frame in the image sequence (starts at 0 and goes as far up as your number of time frames)
  • labelimageId: id of the object in the current timeframe. Will range from 1 .. number_of_objects in the current time frame.
  • trackId: id of the part of the lineage tree. A value of -1 indicates a false detection. An event like appearance, disappearance and division will start a new track.
  • lineageId: id of the linage. All cells that are children of a certain object should have the same lineageId. A value of -1 indicates a false detection
  • parentTrackId: id of the track id of the parent object track (in the previous time frame). If an object divides, there will be two new tracks belonging to the same lineage.

so the linage is basically there.

Cheers

Thank you @k-dominik, this information helps tremendously. Is there a link to the documentation that you can provide that further explains the output in detail or is that still to be completed? Do you mind also elaborating on what mergerLabelId is (I’m assuming it has to do with events such as cell collisions or merging).

So frame makes sense, I can just multiply the frame by my time step size to obtain the time at which that image frame was taken. labelImageId also makes sense: these are just the ids of the objects in the frame. However, is trackId related to the branching of a cell at the division process? Will a root cell always have a trackId of 0? If it divides, will it create trackIds of 1 and 2, wherein those daughter cells will have the same lineageId of the original root cell, but have either trackId of 1 or 2? Could you correct or clarify this for me?

:+1:

:+1:

lowest (regular) value for trackId and lineageId is 2. So if you start with one cell, it will start off with lineageId = 2 and trackId = 2.

This is correct, if you invrement by 2 (so daughter cells should have trackId=3 and trackId=4, whereas the lineageId will remain at 2.

working on it, but not yet there :wink:

Sorry, I missed that one.

mergerId: is the labelimageId of the object that is identified as a merger of multiple ones. For those, new labelImageIds are generated, the mergerId just points to the original one. I guess it’s primary use is to group objects to the same “merge”.

Cheers