Make sure that cellfinder is installed (if not see Installation)
Make sure that your data is organised as expected (see Data requirements)
The cell detection via cellfinder can be run with a single terminal command (
cellfinder -s signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5
Multiple channels can also be processed at once:
cellfinder -s first_signal_channel_images second_signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5
However, there are many options to change what parts of the analysis are run, and how they are run. For instance, to register the brain to the allen reference atlas, use
--register. I recommend looking through the Command line options.
The deep learning network included with cellfinder to classify cells as real cells or artefacts was trained on a very specific dataset. You will very likely need to retrain this if the classification is incorrect on your data. See Training the network.