Detection mCherry cells

For rabies experiments, a separate step is needed to detect starter cells which are usually labelled by the nuclear mCherry native fluorescence. The first step is to detect mCherry cells, which is preprocessing and is described here. The second step, to assign which of these mCherry cells have enough rolonies to be considered rabies positive is already science and out of the scope of iss-preprocess (but see iss-analysis).

Prerequisite

Data must be acquired, projected (using project_and_average) and registered (using register). Registration can be tricky, if it seems to fail, see select_reg_fluorescent_tile_parameters.ipynb for playing with the ops faster.

Automatic detection

        flowchart TD
   start[Start] --> save_unmixing_coefficients
   unmix_coef[calculate_unmixing_coefficient];
       batch_est(((segment_mcherry)));

       subgraph save_unmixing_coefficients
           unmix_coef --> diag_ref([plot_unmixing_diagnostics]);
       end



       unmix_coef --> batch_est;
       batch_est --> remove_all_duplicate_masks;
       style batch_est fill:#E1BEE7,stroke:#424242

       style remove_all_duplicate_masks stroke:#000000,fill:#E1BEE7
       style unmix_coef stroke:#000000,fill:#E1BEE7

       style diag_ref fill:#BBDEFB,stroke:#616161,color:#000000

       style save_unmixing_coefficients fill:#AAAAAA, stroke:#424242