Include `img_sub_folder` as parameter in Mantis calls

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

https://ark-analysis.readthedocs.io/en/latest/

MIT License

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Include `img_sub_folder` as parameter in Mantis calls #1050

Closed alex-l-kong closed 12 months ago

alex-l-kong commented 1 year ago

What is the purpose of this PR?

Closes #1045. Without this argument passed to create_mantis_dir, there isn't a way to copy the single-channel TIF files over.

How did you implement your changes

Added this as a parameter to the function. Additionally, updated cell_clustering_params.json to take in both tiff_dir and img_sub_folder. The former is purely QOL and the latter is to support the img_sub_folder param for the Mantis function in the cell clustering notebook.

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