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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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Unable to load Ilastik crop pipeline file to CellProfiler #132

Closed CodeCheong closed 1 year ago

CodeCheong commented 1 year ago

Hi,

Nice work on developing this pipeline to analyse IMC data! I have been trying to crop images using CellProfiler for Ilastik training. However, I get this error message when importing 1_prepare_ilastik.cppipe:

Error while loading SummarizeStack: Could not find the SummarizeStack module Do you want to stop processing?

Module settings: Ilastik Python Function ScaledMeanPrep lambda x, axis: np.mean(x, axis=axis)*100

When I click on "Analyze Images", nothing is outputted.

May I ask what is the potential error here? Thanks!

nilseling commented 1 year ago

Hi @CodeCheong

it seems like you haven't set up CellProfiler correctly. Please perform step 4 as explained here: https://bodenmillergroup.github.io/ImcSegmentationPipeline/ under Getting started.

CodeCheong commented 1 year ago

Hi @nilseling,

Thanks for the reply, it has worked by following your suggestion. As a side note, may I ask if configuring CellProfiler and setting up the imcsegpipe Conda environment are two different things? Meaning if I have processed the MCD files to the point where I had generated my Ilastik stack, but then found out I haven't yet git cloned hence configured CellProfiler pluggins, will this affect my previous data processing results in any ways? Thanks!

nilseling commented 1 year ago

Both are independent things. So once you have CellProfiler working you can continue with the cropping.