Post clustering functionality #658
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alex-l-kong
requested changes
Aug 17, 2022
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| `cell_segmentation`: This file contains the predicted segmentation for each cell in the image, and allows mantis to identify individual cells. | ||
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| `population_pixel_mask`: This file maps the individual pixel clusters generated by Pixie in the [pixel clustering notebook](link) to the image data. |
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Add the link to the pixel clustering notebook.
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| # generate unique numeric value for each population | ||
| unique_pops = small_table[pop_col].unique() | ||
| small_table['pop_vals'] = small_table[pop_col].replace(to_replace=unique_pops, | ||
| value=list( | ||
| range(1, len(unique_pops) + 1))) |
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Suggested change
| # generate unique numeric value for each population | |
| unique_pops = small_table[pop_col].unique() | |
| small_table['pop_vals'] = small_table[pop_col].replace(to_replace=unique_pops, | |
| value=list( | |
| range(1, len(unique_pops) + 1))) | |
| small_table['pop_vals'] = pd.factorize(small_table[pop_col].tolist())[0] + 1 |
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| def create_mantis_project(cell_table, fovs, seg_dir, pop_col, mask_dir, image_dir, mantis_dir): | ||
| """Creates masks with the updated cell labels""" |
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Needs a more descriptive docstring defining the Args.
alex-l-kong
reviewed
Aug 17, 2022
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@cliu72 @efrancis28 let me know if this makes sense for a post-clustering workflow, any other changes, etc |
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This looks good to me. |
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What is the purpose of this PR?
Adds in logic to annotate the cell table following pixel clustering, as well as detailed instructions for how to use Mantis.
How did you implement your changes
A notebook with two parts. The first allows the user to select subsets of cells, give them new names, and then create a mantis directory to examine them. The second allows the user to identify specific thresholds for functional markers.
Remaining issues
For people who haven't used Mantis, is this clear enough guidance for what they need to do? Are there places where the bare code in the notebook is going to lead to problems? Given that the user is directly manipulating the pandas df there are some inelegant lines still in there, but I couldn't think of a way to avoid it that wasn't super over-engineered.