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Update measure_synapses interface #68

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Merged
merged 5 commits into from
Sep 16, 2025
Merged

Update measure_synapses interface #68

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8a6d819
Update measure_synapses interface
schilling40 Sep 8, 2025
2b7ae50
Feature different resolutions for block extraction
schilling40 Sep 8, 2025
0170c85
Update ChReef cochleae
schilling40 Sep 8, 2025
4087d3b
Various block extractions
schilling40 Sep 16, 2025
17a6778
Merge branch 'master' into update_measure_synapses
schilling40 Sep 16, 2025
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6 changes: 5 additions & 1 deletion flamingo_tools/segmentation/synapse_detection.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -175,14 +175,18 @@ def marker_detection(
if os.path.exists(output_path) and prediction_key in zarr.open(output_path, "r"):
skip_prediction = True

# skip prediction if post-processed output exists
detection_path = os.path.join(output_folder, "synapse_detection.tsv")
if os.path.exists(detection_path):
skip_prediction = True

if not skip_prediction:
prediction_impl(
input_path, input_key, output_folder, model_path,
scale=None, block_shape=block_shape, halo=halo,
apply_postprocessing=False, output_channels=1,
)

detection_path = os.path.join(output_folder, "synapse_detection.tsv")
if not os.path.exists(detection_path):
input_ = zarr.open(output_path, "r")[prediction_key]
detections = find_local_maxima(
Expand Down
41 changes: 41 additions & 0 deletions reproducibility/block_extraction/GEK233L_IHC.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
[
{
"cochlea": "G_EK_000233_L",
"image_channel": [
"Vglut3",
"IHC_v6"
],
"halo_size": [
196,
196,
80
],
"crop_centers": [
[
593,
1018,
276
],
[
674,
1048,
1574
],
[
788,
937,
255
],
[
950,
1450,
380
],
[
1120,
875,
360
]
]
}
]
50 changes: 50 additions & 0 deletions reproducibility/block_extraction/GLR233R_SGN_DA.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
[
{
"cochlea": "G_LR_000233_R",
"image_channel": [
"PV"
],
"halo_size": [
196,
196,
196
],
"crop_centers": [
[
620,
1060,
1050
],
[
1555,
1170,
1230
],
[
1600,
1075,
1090
],
[
1390,
1430,
1375
],
[
650,
1130,
1000
],
[
800,
1230,
710
],
[
600,
1100,
1055
]
]
}
]
36 changes: 36 additions & 0 deletions reproducibility/block_extraction/GLR233R_SGN_train.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
[
{
"cochlea": "G_LR_000233_R",
"image_channel": [
"PV",
"SGN_v2-DA"
],
"halo_size": [
196,
196,
48
],
"crop_centers": [
[
1584,
1570,
958
],
[
1474,
1655,
730
],
[
1275,
1604,
1324
],
[
1603,
1240,
1279
]
]
}
]
25 changes: 25 additions & 0 deletions reproducibility/block_extraction/LaVision-M04_SGN.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
[
{
"cochlea": "LaVision-M04",
"image_channel": [
"PV"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
64
],
"crop_centers": [
[
2550,
2340,
440
]
]
}
]
41 changes: 41 additions & 0 deletions reproducibility/block_extraction/LaVision_IHC_M04.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
[
{
"cochlea": "LaVision-M04",
"image_channel": [
"MYO",
"IHC_LOWRES-v1"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
32
],
"crop_centers": [
[
3118,
2840,
500
],
[
1540,
2075,
924
],
[
2135,
835,
627
],
[
2025,
1332,
221
]
]
}
]
84 changes: 84 additions & 0 deletions reproducibility/block_extraction/LaVision_OTOF_IHC.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
[
{
"cochlea": "LaVision-OTOF23R",
"image_channel": [
"CR",
"IHC_LOWRES-v2"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
48
],
"crop_centers": [
[
1360,
3450,
732
],
[
2408,
913,
688
],
[
2700,
3220,
620
]
]
},
{
"cochlea": "LaVision-OTOF25R",
"image_channel": [
"CR",
"IHC_LOWRES-v2"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
48
],
"crop_centers": [
[
2490,
3460,
875
]
]
},
{
"cochlea": "LaVision-OTOF36R",
"image_channel": [
"CR",
"IHC_LOWRES-v2"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
48
],
"crop_centers": [
[
2558,
3415,
871
]
]
}
]
93 changes: 93 additions & 0 deletions reproducibility/block_extraction/LaVision_SGN_empty.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,93 @@
[
{
"cochlea": "LaVision-M04",
"image_channel": [
"PV"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
64
],
"crop_centers": [
[
396,
1906,
383
],
[
830,
3390,
670
],
[
3520,
1525,
310
],
[
1867,
2538,
390
],
[
400,
2500,
840
]
]
},
{
"cochlea": "LaVision-Mar05",
"image_channel": [
"PV"
],
"resolution" : [
1.887779,
1.887779,
3.0
],
"halo_size": [
128,
128,
64
],
"crop_centers": [
[
2247,
2434,
1660
],
[
1182,
2920,
726
],
[
2530,
1660,
1840
],
[
620,
1900,
1825
],
[
1330,
3375,
1114
],
[
3442,
2950,
1000
]
]
}
]
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