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+16,14.0,149.57199545369448,,,,,39.0,167.86077531097013,37,174.35990801786974 +17,12.0,170.03345068544604,,,,,3.0,197.68199389929276,26,192.21918426629537 +18,11.0,170.26763221469898,,,,,30.0,199.64515666551995,38,193.06534764167287 +19,5.0,180.93926111267285,,,,,,,36,193.95762797064725 +20,,,,,,,,,20,198.12128776080576 diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv new file mode 100644 index 0000000..6e9cb50 --- /dev/null +++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv @@ -0,0 +1,6 @@ +,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,D_SNAP25_12.08.12_KO1.1_3_crop_diameter,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,C_SNAP25_12082_KO1.2_6_crop_diameter,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_diameter,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_diameter,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_diameter +0,9,9.193587982936805,56.26909744547573,4,1.554,47.81289742868499,8,3.4748496370346733,54.5150906509724,13.0,4.662,49.91813042345726,1.0,6.216,62.88804789234515 +1,10,10.878,59.8139155734108,9,1.554,50.26043018499918,6,5.154034924212291,50.26043018499918,1.0,7.77,47.81289742868499,27.0,10.308069848424582,57.37547691442199 +2,13,12.90849348297469,62.34039118335815,7,4.662,46.96871937691663,11,6.216,58.36307916126143,9.0,9.452612972083434,46.96871937691663,,, +3,15,14.660406679215962,49.91813042345726,8,6.216,57.37547691442199,12,6.407306142209845,56.26909744547573,11.0,11.419521180855176,51.49606651201725,,, +4,18,22.46591738612069,64.59166755828387,5,13.636294658007358,51.71755599228722,14,6.407306142209845,57.37547691442199,,,,,, diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv new file mode 100644 index 0000000..43211cc --- /dev/null +++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv @@ -0,0 +1,6 @@ +,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance +0,9,9.193587982936805,4,1.554,8,3.4748496370346733,13.0,4.662,1.0,6.216 +1,10,10.878,9,1.554,6,5.154034924212291,1.0,7.77,27.0,10.308069848424582 +2,13,12.90849348297469,7,4.662,11,6.216,9.0,9.452612972083434,, +3,15,14.660406679215962,8,6.216,12,6.407306142209845,11.0,11.419521180855176,, +4,18,22.46591738612069,5,13.636294658007358,14,6.407306142209845,,,, diff --git a/scripts/cooper/run_compartment_segmentation.py b/scripts/cooper/run_compartment_segmentation.py index 6396fd1..d4d3589 100644 --- a/scripts/cooper/run_compartment_segmentation.py +++ b/scripts/cooper/run_compartment_segmentation.py @@ -15,7 +15,7 @@ def run_compartment_segmentation(args): model_path = args.model segmentation_function = partial( - segment_compartments, model_path=model_path, verbose=False, tiling=tiling, scale=[0.25, 0.25, 0.25] + segment_compartments, model_path=model_path, verbose=False, tiling=tiling, scale=[0.25, 0.25, 0.25], boundary_threshold=args.boundary_threshold ) inference_helper( args.input_path, args.output_path, segmentation_function, force=args.force, data_ext=args.data_ext @@ -50,6 +50,9 @@ def main(): parser.add_argument( "--data_ext", default=".mrc", help="The extension of the tomogram data. By default .mrc." ) + parser.add_argument( + "--boundary_threshold", type=float, default=0.4, help="Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM." + ) args = parser.parse_args() run_compartment_segmentation(args) diff --git a/synapse_net/inference/compartments.py b/synapse_net/inference/compartments.py index 0826827..113230f 100644 --- a/synapse_net/inference/compartments.py +++ b/synapse_net/inference/compartments.py @@ -155,6 +155,7 @@ def segment_compartments( scale: Optional[List[float]] = None, mask: Optional[np.ndarray] = None, n_slices_exclude: int = 0, + boundary_threshold: float=0.4, **kwargs, ) -> Union[np.ndarray, Tuple[np.ndarray, np.ndarray]]: """Segment synaptic compartments in an input volume. @@ -168,6 +169,7 @@ def segment_compartments( return_predictions: Whether to return the predictions (foreground, boundaries) alongside the segmentation. scale: The scale factor to use for rescaling the input volume before prediction. n_slices_exclude: + boundary_threshold: Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM. Returns: The segmentation mask as a numpy array, or a tuple containing the segmentation mask @@ -193,9 +195,9 @@ def segment_compartments( # We may want to expose some of the parameters here. t0 = time.time() if input_volume.ndim == 2: - seg = _segment_compartments_2d(pred) + seg = _segment_compartments_2d(pred, boundary_threshold=boundary_threshold) else: - seg = _segment_compartments_3d(pred, n_slices_exclude=n_slices_exclude) + seg = _segment_compartments_3d(pred, n_slices_exclude=n_slices_exclude, boundary_threshold=boundary_threshold) if verbose: print("Run segmentation in", time.time() - t0, "s")