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!