How to get started with cellfinder
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 -v 5 2 2 --orientation psl
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 -v 5 5 2 --orientation psl
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.