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Tonotopic mapping with multiple components #63

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Merged
merged 11 commits into from
Aug 21, 2025
Merged

Tonotopic mapping with multiple components #63

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ef31759
Tonotopic mapping with multiple components
schilling40 Aug 18, 2025
a6ce26b
Dictionaries for block extraction, tonotopic mapping, and object meas…
schilling40 Aug 18, 2025
cdad8a6
Added blocks for torn components
schilling40 Aug 19, 2025
04d0c5f
Added documentation
schilling40 Aug 19, 2025
533f8e4
Object measures for torn components
schilling40 Aug 20, 2025
8a8348f
Option to specify components for identifying central path
schilling40 Aug 21, 2025
28d5c21
Update Greenwood function
schilling40 Aug 21, 2025
3bce163
Fixed factor in Greenwood function
schilling40 Aug 21, 2025
722dcec
Update dictionaries
schilling40 Aug 21, 2025
6b13170
Adapted tonotopic bins
schilling40 Aug 21, 2025
c0ec6fd
Merge branch 'master' into mapping_multiple_components
constantinpape Aug 21, 2025
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407 changes: 316 additions & 91 deletions flamingo_tools/segmentation/cochlea_mapping.py
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63 changes: 63 additions & 0 deletions reproducibility/block_extraction/ChReef_GEK49L.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
[
{
"cochlea": "G_EK_000049_L",
"image_channel": [
"GFP",
"PV",
"SGN_v2"
],
"segmentation_channel": "SGN_v2",
"type": "sgn",
"n_blocks": 8,
"halo_size": [
256,
256,
50
],
"component_list": [
1
],
"crop_centers": [
[
1019,
1459,
2580
],
[
1390,
1557,
2309
],
[
1106,
1680,
1897
],
[
615,
1467,
1896
],
[
591,
1027,
2185
],
[
1064,
791,
2205
],
[
1474,
810,
1834
],
[
1584,
991,
1347
]
]
}
]
39 changes: 39 additions & 0 deletions reproducibility/block_extraction/ChReef_GEK49L_torn_components.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
[
{
"cochlea": "G_EK_000049_L",
"image_channel": [
"GFP",
"PV",
"SGN_v2"
],
"segmentation_channel": "SGN_v2",
"component_list": [
3,
4,
5
],
"type": "sgn",
"halo_size": [
256,
256,
50
],
"crop_centers": [
[
1025,
1160,
1155
],
[
1085,
895,
995
],
[
830,
515,
955
]
]
}
]
63 changes: 63 additions & 0 deletions reproducibility/block_extraction/ChReef_GEK49R.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
[
{
"cochlea": "G_EK_000049_R",
"image_channel": [
"GFP",
"PV",
"SGN_v2"
],
"segmentation_channel": "SGN_v2",
"type": "sgn",
"n_blocks": 8,
"halo_size": [
256,
256,
50
],
"component_list": [
1
],
"crop_centers": [
[
1300,
1538,
1377
],
[
1479,
1118,
1468
],
[
1124,
1128,
1020
],
[
620,
1275,
1326
],
[
796,
1019,
1809
],
[
1029,
499,
1628
],
[
860,
170,
1115
],
[
288,
198,
924
]
]
}
]
27 changes: 27 additions & 0 deletions reproducibility/block_extraction/ChReef_GEK49R_torn_components.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
[
{
"cochlea": "G_EK_000049_R",
"image_channel": [
"GFP",
"PV",
"SGN_v2"
],
"segmentation_channel": "SGN_v2",
"component_list": [
2
],
"type": "sgn",
"halo_size": [
256,
256,
50
],
"crop_centers": [
[
645,
435,
815
]
]
}
]
55 changes: 55 additions & 0 deletions reproducibility/block_extraction/ChReef_MLR153L.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
[
{
"cochlea": "M_LR_000153_L",
"image_channel": [
"PV",
"GFP",
"SGN_v2"
],
"segmentation_channel": "SGN_v2",
"type": "sgn",
"n_blocks": 6,
"halo_size": [
256,
256,
50
],
"component_list": [
1,
2,
3
],
"crop_centers": [
[
1225,
638,
807
],
[
1310,
378,
878
],
[
1152,
239,
1061
],
[
860,
186,
1052
],
[
830,
297,
692
],
[
1073,
325,
448
]
]
}
]
41 changes: 41 additions & 0 deletions reproducibility/block_extraction/GEK11R_Myo7a.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
[
{
"cochlea": "G_EK_000011_R",
"image_channel": [
"Myo7a_resized",
"IHC_resized_v4b"
],
"segmentation_channel": "IHC_resized_v4b",
"type": "ihc",
"halo_size": [
256,
256,
50
],
"component_list": [
1
],
"crop_centers": [
[
1300,
1780,
1320
],
[
1500,
1270,
1500
],
[
1530,
1440,
540
],
[
930,
550,
1940
]
]
}
]
55 changes: 55 additions & 0 deletions reproducibility/block_extraction/MLR215R_CR.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
[
{
"cochlea": "M_LR_000215_R",
"image_channel": [
"CR",
"IHC_v4b"
],
"segmentation_channel": "IHC_v4b",
"type": "ihc",
"n_blocks": 6,
"halo_size": [
256,
256,
50
],
"component_list": [
7,
4,
1,
11
],
"crop_centers": [
[
464,
1233,
828
],
[
1106,
1007,
821
],
[
670,
438,
1048
],
[
273,
931,
671
],
[
934,
937,
293
],
[
1167,
259,
591
]
]
}
]
16 changes: 16 additions & 0 deletions reproducibility/object_measures/ChReef_GEK49L.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
[
{
"cochlea": "G_EK_000049_L",
"image_channel": [
"GFP"
],
"segmentation_channel": "SGN_v2",
"background_mask": "yes",
"component_list": [
1,
3,
4,
5
]
}
]
14 changes: 14 additions & 0 deletions reproducibility/object_measures/ChReef_GEK49R.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
[
{
"cochlea": "G_EK_000049_R",
"image_channel": [
"GFP"
],
"segmentation_channel": "SGN_v2",
"background_mask": "yes",
"component_list": [
1,
2
]
}
]
13 changes: 13 additions & 0 deletions reproducibility/object_measures/SGNsubtype_MAMDN62L.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
[
{
"cochlea": "M_AMD_N62_L",
"image_channel": [
"Calb1",
"CR"
],
"segmentation_channel": "PV_SGN_v2",
"component_list": [
1
]
}
]
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