ClassifyPixels - what is the input image from Ilastik?

Hey all

I’m using Ilastik 1.1 to classify pixels and then I want to import the classifiers in CellProfiler.
My question is: how can I export classifier files from Ilastik? When I look at the export options in Ilastik I find: “probabilities”, “simple segmentation”, “uncertainty” and “features”. Which one should I chose?


Hi Cristina,

Unfortunately CellProfiler does not yet support ilastik 1.0+. We are working on it! …but it adds a lot of dependencies (i.e. it’s hard).
You can use the ilastik that comes bundled with CellProfiler, though the interfere is substantially different than 1.0+. There is an “Export classifier” button in the Classify tab in ilastik (I think that’s right, or close at least).

Hope that helps,

Hi David

Thank you for your answer. I’ve tested Ilastik v0.5, but my cells are too small and, because 0.5 does not allow changing the brush to a smaller size, i can’t use it.
I’ve found a workaround though, so I can use Ilastik v.1.1 for segmentation and then CellProfiler for further analysis:

  • I’m using the “Pixel classification + Object classification” module from Ilastik v.1.1, to define objects
  • I export the objects as images (function: export object probabilities); because the export function is active only when I first classify the objects, I do a mock classification. Thus, in the resulting image some objects will be grey, some white, and black background
  • I’m importing the object images into CellProfiler and I use “CorrectIlluminationApply” module, to make all objects white and the background black
  • then I use the “identifty primary objects” module - because now the objects are white and separated by black background, this works quite well
  • and then I go on with downstream analysis

Hopefully in the future a easier way to transfer objects from Ilastik v1.1 to CellProfiler will become available.
And by the way, the CellProfiler team has done some AWESOME work! In the last weeks I’ve tested several software for image analysis, and CellProfiler is by far my first choice. Before I was contemplating writing my own Mathlab code (which makes me deeply unhappy, as it takes away from my lab and microscopy time). Now, with CellProfiler there is no need for that!


Hi Cristina,

It certainly does! Just right-click on the image and you get a menu like this (attached screenshot).

But otherwise your workaround sounds reasonable, if cumbersome. I have also pondered exporting ilastik 1.1 output,
but was thinking of just the probability maps, and then use those as input to CellProfiler. I may be biased (wink) but I prefer the segmentation flexibility in CellProfiler given a continuous input like probability maps, rather than the objects themselves. But if it works for you, great. And yes, we realize the need for ilastik 1.1+ support in CP!