I want to track cells and within those cells quantify the number of spots.
Channel 1: DNA for cell segmentation and tracking
Channel2 : spots to be counted/analyseed in CellProfiler
I am using multiple softwares for different purposes / trials
- Ilastik Pixel Classifier first to generate segmentation, and then the Ilastik tracking module.
- fiji to analyse the tracks with MaMuT/TrackMate and hopefully correct some divisions/daughters mis-assignement
- cell profiler to use the corrected probability masks and tracks (from MaMuut) in channel 1 but count spots in channel 2.
Data Preparation - H5 format
it seems I have and hdf5 conversion problem.
For TrackMate/MaMut, I need to use the BigDataViewer to export into hdf5 and xml (otherwise I can’t export the tracks in the Ilastik Fiji/Mamut plugin version). So I exported my channels separately using the bigdataviewer
But I trained the pixel classifier and tracking in IIlastik using h5 data subset from Fiji ilastik plugin
pixel classification - tracking in Ilastik
I trained the classifier on a subset of my movies that were exported into h5 using the fiji-ilastik export module.
I then went on to the Ilastik Tracking module which worked nicely.
I wanted to export in a format compatible for MaMut but it did not work as I did not have the xml file (that needs to be generateed with BigDataViewer - hence point 1).
So I went back to data I havent analysed yet, converted data to h5 using the bigDataViewer and wanted to batch process them using the Ilastik Pixel classifier, but I got an error message
Is this because the classifier was trained on an h5 image that came from a different source (Ilastik Fiji plugin vs BigData Viewer)?
- export of probabilities map /tracks to Cell Profiler
After checking the tracks of channel 1 with trackmate (and correct them??), I would like to use CP to analyse the 2nd channel.
Would that be the correct export setup (then used for batch files)?
Would it be doable to export tracks and object IDs
On a side note: I have just been playing with Ilastik for the past day and am really pleased with how well it all works!!