Cell detection and analysis without cell classification

[PedjaJJ]

Is your feature request related to a problem? Please describe. In current version it is not possible to get just cell detection and cell analysis without cell classification. This could be potentially beneficial if you are analyzing cFos (nuclear) staining. With parameters that can be changed in cellfinder now I was able to get very good cFos detection results. When classification is done more than half of this cells are removed.

Describe the solution you'd like I would like to see solution that will enable me to have all detected cells classified as cells and then proceed to analysis step

Describe alternatives you've considered I tried changing output files (cells.xml to cell_calssifiction.xml and vice versa) but in first case he skips analysis cause no cells were detected and in the other he is running cell classification Additional context Add any other context or screenshots about the feature request here.

[adamltyson]

If anyone wants to tackle this, the steps should be:

• Add a command line flag to the parser
• Add some logic to main.py to skip classification, but load the cell candidates from cells.xml as cells
• Run analysis as normal
• Add options to docs

As an aside @PedjaJJ, I'd love to see how well cellfinder is working with cfos data without classification. If you're able to share some data (even just a part of a brain), it would be great to add this workflow as an example/tutorial to the documentation.