Make segmentation_dir definition more clear for pixel and cell clustering processes
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@cliu72 just realized I need to address one final path related issue to deepcell output, holding off on the review for now. |
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@cliu72 had to ensure that on the example dataset, |
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What is the purpose of this PR?
Closes #844. Makes sure the nomenclature of
segmentation_diris more consistent between the notebooks.How did you implement your changes
@cliu72 summarized the changes in a comment on that thread. Essentially we'll be removing any explicit mention of
deepcellin notebook variables. We'll also make suresegmenation_diractually points to the segmentation directory (and not the root directory containing the segmentation and cell table directories in the example dataset).