Comments (3)
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
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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!
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Both are independent things. So once you have CellProfiler working you can continue with the cropping.
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Related Issues (20)
- Cell segmentation in placental cells. HOT 2
- Error while loading summarizestack HOT 3
- Creating unique .h5 files for Ilastik from ImcSegmentationPipeline Jupyter notebook HOT 2
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- Switch use of readimc in pipeline HOT 1
- Error installing conda environment HOT 7
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- Nd145 not in list error when generating image stacks HOT 5
- Error“Generate image stacks for downstream analyses” HOT 13
- single-cell expression data HOT 1
- Presence of undefined channels during conversion from MCD to ome-TIFF HOT 2
- Numpy float or unsigned integer in TIFF images HOT 3
- Jupyter-lab did not open Jupyter notebook HOT 5
- TIFF output all black HOT 4
- windows zip file compression type not recognized
- Corrupt MCD file - using .txt instead HOT 4
- Error in 3_measure_mask.cppipe HOT 4
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