diff --git a/brainglobe_workflows/cellfinder/cellfinder_main.py b/brainglobe_workflows/cellfinder/cellfinder_main.py index 7f8845fa..928b1786 100644 --- a/brainglobe_workflows/cellfinder/cellfinder_main.py +++ b/brainglobe_workflows/cellfinder/cellfinder_main.py @@ -19,11 +19,11 @@ class Workflow: """ - Defines the cellfinder workflow built around running the + Defines the cellfinder workflow built around running the cellfinder_core.main.main() function. - It includes `setup` methods that encapsulate steps which are required - to run the workflow, but that we don't expect to benchmark + It includes `setup` methods that encapsulate steps which are required + to run the workflow, but that we don't expect to benchmark (such as defining processing parameters or downloading the test data). """ @@ -107,6 +107,7 @@ def setup_input_data(self): if f.startswith(self.background_parent_dir) ] + def workflow_from_cellfinder_run(cfg): """ Run workflow based on the cellfinder_core.main.main() @@ -135,9 +136,7 @@ def workflow_from_cellfinder_run(cfg): # Run main analysis using `cellfinder_run` detected_cells = cellfinder_run( - signal_array, - background_array, - cfg.voxel_sizes + signal_array, background_array, cfg.voxel_sizes ) # Save results to xml file