ritvikvasan
commented
3 years ago I tried adding pytorch_integrated_cell to the setup requirements via "pytorch_integrated_cell @ git+https://git@github.com/AllenCellModeling/pytorch_integrated_cell#egg=pytorch_integrated_cell" in one of the requirement lists, but i get a bunch of weird import errors. I havent pushed this -- Im still checking how to add this
Pull request recommendations:
[ ] Name your pull request your-development-type/short-description. Ex: feature/read-tiff-files
[ ] Link to any relevant issue in the PR description. Ex: Resolves [gh-12], adds tiff file format support
[ ] Provide context of changes.
[ ] Provide relevant tests for your feature or bug fix.
[ ] Provide or update documentation for any feature added by your pull request.
Added the generate_gfp_instantiations step to generate a specificied number of structures using Greg's trained 3D IC model from a specific CellID.
Added the multi_res_struct_compare step to compute Pearson Correlation between similar structures generated via IC
Added the multi_res_cross_corr step to compute Pearson Correlation between dissimilar structures generated via IC
Added the make_diagnostic_sheet step to make contact sheets in the HTML format that Matheus designed. Has 2 specifications - projection_channel == "seg" will make a plot of the nucleus and membrane contour + structure gfp channel. projection_channel == "raw" (or anything else) will make a max project of nucleus, membrane, and structure gfp channel.
TO DO: We need to resolve torch dependencies for IC, either change the CI yaml file or move torch deps to the main deps list
Thanks for contributing!