Introduce a new parameter --output-format that allows users to control how the output will be written. By default, it can be CSV for simple cases (e.g., one mask, one metric) and AnnData for more complex processing (e.g., multiple masks/metrics, with and without background subtraction, with and without log transformation, etc.)
Introduce a new parameter
--output-formatthat allows users to control how the output will be written. By default, it can be CSV for simple cases (e.g., one mask, one metric) and AnnData for more complex processing (e.g., multiple masks/metrics, with and without background subtraction, with and without log transformation, etc.)