ImcSegmentationPipeline

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Better error handling

5

Currently, the error capturing is implemented to catch all errors and notify the user that an error happened, but the actual error is not displayed, which makes it difficult to...

votti

Question on the identifySecondaryObject in the CellProfiler Pipeline (general question )

3

Hi. so my question is, 'how important is the 'identifySecondaryObject' / ImageMath module for the CP segmentation step using the bodenmiller pipeline? If i use nuclei as primary objects alone,...

arcolombo

Error when creating spatial experiment object from IMC segmentation pipeline: 'Could not guess delimiter'.

1

I tried to generate a spatial experiment object 'spe2' as per instructions in 5.1.2: https://bodenmillergroup.github.io/IMCDataAnalysis/read-data.html. 'Error: Could not guess the delimiter. Use `vroom(delim =)` to specify one explicitly.' Has anyone...

AnanyaBhalla

hi when i compress my mcd/txt files using windows defaults i get the below message in jypter . it mentions the lzma compression type, so i don't know the zipfile...

arcolombo

1_prepare_ilastik.cppipe pipeline not working

6

Hi pipeline creator, I am new to IMC data analysis so please bear my ignorance. My query related to this- https://bodenmillergroup.github.io/ImcSegmentationPipeline/ilastik.html While trying to import 1_prepare_ilastik.cppipe pipeline into cellprofiler, i...

akedarg