Provide an option to move the mask suffix from column names to filenames
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Currently, the module tags each column with a suffix that specifies which mask was used during quantification, e.g., Hoechst0_cellMask, CD20_nucleiMask, etc. This creates a mismatch between column names and marker names in markers.csv, requiring all downstream modules to perform additional processing.
TODO: Add a command-line option that moves the mask suffix from column names to filenames. In other words, instead of producing a single exemplar-001.csv that contains columns CD45_cellMask, CD45_nucleiMask, etc., have the tool output multiple files, exemplar-001_cellMask.csv, exemplar-001_nucleiMask.csv, etc., with each file containing the column CD45, which will be a direct match against the names in markers.csv.
As a bonus, multiple files will provide morphological features for the different masks, allowing one to compare, e.g., the ratio of nucleus and cytoplasm areas.
Addressed in #29