From 190cae55bc134246250eb717239499a6393d2513 Mon Sep 17 00:00:00 2001 From: ngreenwald Date: Wed, 23 Sep 2020 10:43:39 -0700 Subject: [PATCH] updated params --- .../applications/multiplex_segmentation.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/deepcell/applications/multiplex_segmentation.py b/deepcell/applications/multiplex_segmentation.py index 84efa631f..b6de116e4 100644 --- a/deepcell/applications/multiplex_segmentation.py +++ b/deepcell/applications/multiplex_segmentation.py @@ -185,16 +185,18 @@ def predict(self, """ if postprocess_kwargs_whole_cell is None: - postprocess_kwargs_whole_cell = {'maxima_threshold': 0.05, 'maxima_model_smooth': 0, - 'interior_model_smooth': 2, 'interior_threshold': 0.2, - 'small_objects_threshold': 10, - 'fill_holes_threshold': 10} + postprocess_kwargs_whole_cell = {'maxima_threshold': 0.1, 'maxima_model_smooth': 0, + 'interior_threshold': 0.3, 'interior_model_smooth': 2, + 'small_objects_threshold': 15, + 'fill_holes_threshold': 15, + 'radius': 2} if postprocess_kwargs_nuclear is None: - postprocess_kwargs_nuclear = {'maxima_threshold': 0.05, 'maxima_model_smooth': 0, - 'interior_model_smooth': 2, 'interior_threshold': 0.3, - 'small_objects_threshold': 10, - 'fill_holes_threshold': 10} + postprocess_kwargs_nuclear = {'maxima_threshold': 0.1, 'maxima_model_smooth': 0, + 'interior_threshold': 0.3, 'interior_model_smooth': 2, + 'small_objects_threshold': 15, + 'fill_holes_threshold': 15, + 'radius': 2} # create dict to hold all of the post-processing kwargs postprocess_kwargs = {'whole_cell_kwargs': postprocess_kwargs_whole_cell,