Add workflows for QuPath, napari and ilastik

pr4deepr / GutAnalysisToolbox

Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.

https://gut-analysis-toolbox.gitbook.io/docs/

BSD 3-Clause "New" or "Revised" License

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Add workflows for QuPath, napari and ilastik #5

Open pr4deepr opened 2 years ago

pr4deepr commented 2 years ago

Add neuron subtype segmentation workflow in QuPath
Add neuron segmentation , subtype segmentation using StarDist and downstream analysis using pyclesperanto assistant in napari

pr4deepr commented 2 years ago

ilastik has a nice workflow for counting cells that is perfect for enteric neurons: https://www.ilastik.org/documentation/counting/counting