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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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Error in 3_measure_mask.cppipe #138

Closed Acaro12 closed 4 months ago

Acaro12 commented 5 months ago

Hi,

I am getting an error when performing the last step of the Preprocessing pipeline which is the cellprofiler pipeline 3_measure_mask.cppipe. During postprocessing the following error occurs:

"Encountered uncrecoverable error in ExportVarCsv during post-processing: list index out of range"

Apparently, this prevents the pipeline from generating these two files: Var_Image.csv Var_cell.csv

I adapted the number of markers (16) in the pipeline settings.

What could have caused this problem?

Thank you in advance,

Christoph

Acaro12 commented 5 months ago

Hi again,

I'd really appreciate some help with this issue.

I attached a small data sample (cpout, cpinp) which generates the same error when running 3_measure_mask.cppipe

Any idea what causes this? @Milad4849 , you helped with another issue - maybe you know what is going on here?

Thank you in advance,

Christoph [Uploading Reprex.zip…]()

Milad4849 commented 5 months ago

@Acaro12 I think something went wrong with the attachment, could you reattach it? I can have a look, however ImcSegmentationPipeline is soon to be deprecated and longer supported. So maybe this is a good time to move over to steinbock.

Milad4849 commented 4 months ago

is there still an issue?

Milad4849 commented 4 months ago

Closing due to inactivity