Cell In[6], line 1 the paths with the ziped acquisition files ^ SyntaxError: invalid syntax

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Cell In[6], line 1 the paths with the ziped acquisition files ^ SyntaxError: invalid syntax #115

Closed svelagala007 closed 1 year ago

svelagala007 commented 1 year ago

Hi, as I'm running through the code, I am receiving this error message. How would I be able to fix this? Thanks

nilseling commented 1 year ago

Hi @svelagala007, could you please post a screenshot of your jupyter session here?

svelagala007 commented 1 year ago

I'm not sure if I have added too many codes here...

svelagala007 commented 1 year ago

nilseling commented 1 year ago

Hi @svelagala007

steps 1. to 5. here are not performed in jupyter notebook. Once you have activated your conda environment you can open jupyer-lab and use it to open the imc_preprocessing.py script. In this script you will only need to adjust the paths to where your data lies. You will not need to add more code chunks.

svelagala007 commented 1 year ago

Thank you! I will do that!

nilseling commented 1 year ago

Assuming this has been resolved - closing now. Please reopen if it's still an issue.