To use Trainable Weka Segmentation within CellProfiler

I am using Trainable weka Segmentaion plugin in Fiji for segmentation. I am interested to use CellProfiler to find cell count, area etc. Is there any module available to use this plugin within cellprofiler for automatic prediction like classifypixels for ilastik? If not is there any other possibility? I have attached my Image(Preprocessed-cropped and shading corrected,composite) in which blue channel(Cell Trace Violett dye ) corresponds to living cells and green channel (HiLyte dye)corresponds to tracks caused by movement of cells.


You can use the CellProfiler module called RunImageJ to run commands and scripts on ImageJ/FIJI plugins. However, the Weka plugin is a complicated one, and doesn’t just take an image in and then make a transformation and then output an image. Just like with ilastik and CellProfiler, if you want to apply your classifier from a small training set of images onto a new, untrained test set, then you can’t use the RunImageJ schema in CellProfiler (unless someone else has a brilliant idea!). You would need to save the classifier and then apply it within CellProfiler, which is not implemented in CP.

As a not-so-great hack, you could do all your training and application of the Weka classifier within FIJI, then save off the probability maps for each and every image in your test set. Then you could use those as separate inputs into a CellProfiler pipeline and do segmentation using the probability maps.

So I guess the obvious question is: why not use ilastik+CP, which can accomplish much the same result? (Well, I have never used the Weka Trainable Segmentation except for a few minutes ago, so please tell me if I’m missing something!)


Hi David,

Thanks for your reply. I was using Ilastik and CellProfiler combination for my image analysis but I need some pre-processing steps like cropping with rounded rectangle tool , shading correction, Merge different channels etc for my images which I am doing with Fiji. I thought if there is a possibility to use trainable Weka Plugin of Fiji within CellProfiler using RunImageJ module,I can consolidate the tools. (Fiji - preprocessing and classification in training images, CellProfiler- prediction and analysis all in a single pipeline). At present in CellProfiler, Ilastik 0.5 version can only be used which has memory constraints. I am not able to use more images for training. Is there a possibility to use the current version of Ilastik within CellProfiler?


It’s not possible right now, but it’s high on our list, and has been awhile:

It’s not as easy as it sounds to integrate these two large software package dependencies, so bear with us!