Example pipeline with Ilastik mask imports?


is there an example pipeline with Ilastik input?
I have nuclear masks of a timelapse and I would like to use those to analyse a 2nd channel (count speckles). But unsure how to integrate Ilastik in it.

Also any training course of CellProfiler in Europe?


It seems to me you do not necessarily need ilastik for this task.
Although, if you insist on using it. I believe the Object classification workflow is what you need.
You can import your nuclear masks in the segmentation image section at the first step. Of course, your raw data of the “2nd channel” in Raw data section.

If your speckles are not segmented. You will have to train your classifier in the following step. Once done, you may only need to export the object feature table to .csv or whatever you want.

I don’t really understand what you want to do with the 2nd channel. Just counting the number of speckles ? If so, image
The number of holes seems to be close to what you need.
To note, I’m not sure about the last part, you may have to invert the image before counting.


thanks for the link!
what alternative to Ilastik can I use within CP?
I like the fact that dividing cells in Ilastik get the same “color” label as the parent so easier to track “lineage” but if there is an inbuilt module in CP, I am all up for it…
I segment & track the cells using DNA in channel 1 and will have to segment & count the speckles in channel 2.


What I would do is:

  1. Segment both DNA and speckle to get masks
  2. Label both masks
  3. Count for each DNA region, the numbers inside them

Of course, this requires a bit of programming.

I’m not a CP user. I can not help you on that. I believe @bcimini will tell you all about CP.