Merge branch 'main' of https://github.com/computational-cell-analytics/synaptic-reconstruction

Author: constantinpape

environment.yaml

@@ -8,5 +8,9 @@ dependencies:
     - pip
     - pyqt
     - magicgui
+    - pytorch
+    - bioimageio.core
+    - kornia
+    - tensorboard
     - pip:
         - napari-skimage-regionprops

run_correction.sh

@@ -8,7 +8,7 @@
 import numpy as np
 import pandas
 
-from synaptic_reconstruction.distance_measurements import create_object_distance_lines
+from synaptic_reconstruction.distance_measurements import create_object_distance_lines, load_distances
 from synaptic_reconstruction.file_utils import get_data_path
 from synaptic_reconstruction.tools.distance_measurement import _downsample
 
@@ -21,11 +21,12 @@
 def get_distance_visualization(
     tomo, segmentations, distance_paths, vesicle_ids, scale, return_mem_props=False
 ):
-    ribbon_lines, _ = create_object_distance_lines(distance_paths["ribbon"], seg_ids=vesicle_ids, scale=scale)
-    pd_lines, _ = create_object_distance_lines(distance_paths["PD"], seg_ids=vesicle_ids, scale=scale)
-    membrane_lines, mem_props = create_object_distance_lines(
-        distance_paths["membrane"], seg_ids=vesicle_ids, scale=scale
-    )
+    d, e1, e2, ids = load_distances(distance_paths["ribbon"])
+    ribbon_lines, _ = create_object_distance_lines(d, e1, e2, ids, filter_seg_ids=vesicle_ids, scale=scale)
+    d, e1, e2, ids = load_distances(distance_paths["PD"])
+    pd_lines, _ = create_object_distance_lines(d, e1, e2, ids, filter_seg_ids=vesicle_ids, scale=scale)
+    d, e1, e2, ids = load_distances(distance_paths["membrane"])
+    membrane_lines, mem_props = create_object_distance_lines(d, e1, e2, ids, filter_seg_ids=vesicle_ids, scale=scale)
 
     distance_lines = {
         "ribbon_distances": ribbon_lines,

scripts/inner_ear/check_results.py

@@ -8,13 +8,15 @@
     name="synaptic_reconstruction",
     packages=find_packages(exclude=["test"]),
     version=__version__,
-    author="Constantin Pape; Sarah Muth",
+    author="Constantin Pape; Sarah Muth; Luca Freckmann",
     url="https://github.com/computational-cell-analytics/synaptic_reconstruction",
     license="MIT",
     entry_points={
         "console_scripts": [
-            "sr_tools.correct_segmentation = synaptic_reconstruction.tools.segmentation_correction:main",
-            "sr_tools.measure_distances = synaptic_reconstruction.tools.distance_measurement:main",
-        ]
+            "synapse_net.run_segmentation = synaptic_reconstruction.tools.cli:segmentation_cli"
+        ],
+        "napari.manifest": [
+            "synaptic_reconstruction = synaptic_reconstruction:napari.yaml",
+        ],
     },
 )