Skip to content

Commit ff84404

Browse files
Merge pull request #63 from computational-cell-analytics/mapping_multiple_components
Tonotopic mapping with multiple components
2 parents 9556955 + c0ec6fd commit ff84404

20 files changed

+784
-96
lines changed

flamingo_tools/segmentation/cochlea_mapping.py

Lines changed: 316 additions & 91 deletions
Large diffs are not rendered by default.
Lines changed: 63 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_L",
4+
"image_channel": [
5+
"GFP",
6+
"PV",
7+
"SGN_v2"
8+
],
9+
"segmentation_channel": "SGN_v2",
10+
"type": "sgn",
11+
"n_blocks": 8,
12+
"halo_size": [
13+
256,
14+
256,
15+
50
16+
],
17+
"component_list": [
18+
1
19+
],
20+
"crop_centers": [
21+
[
22+
1019,
23+
1459,
24+
2580
25+
],
26+
[
27+
1390,
28+
1557,
29+
2309
30+
],
31+
[
32+
1106,
33+
1680,
34+
1897
35+
],
36+
[
37+
615,
38+
1467,
39+
1896
40+
],
41+
[
42+
591,
43+
1027,
44+
2185
45+
],
46+
[
47+
1064,
48+
791,
49+
2205
50+
],
51+
[
52+
1474,
53+
810,
54+
1834
55+
],
56+
[
57+
1584,
58+
991,
59+
1347
60+
]
61+
]
62+
}
63+
]
Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_L",
4+
"image_channel": [
5+
"GFP",
6+
"PV",
7+
"SGN_v2"
8+
],
9+
"segmentation_channel": "SGN_v2",
10+
"component_list": [
11+
3,
12+
4,
13+
5
14+
],
15+
"type": "sgn",
16+
"halo_size": [
17+
256,
18+
256,
19+
50
20+
],
21+
"crop_centers": [
22+
[
23+
1025,
24+
1160,
25+
1155
26+
],
27+
[
28+
1085,
29+
895,
30+
995
31+
],
32+
[
33+
830,
34+
515,
35+
955
36+
]
37+
]
38+
}
39+
]
Lines changed: 63 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_R",
4+
"image_channel": [
5+
"GFP",
6+
"PV",
7+
"SGN_v2"
8+
],
9+
"segmentation_channel": "SGN_v2",
10+
"type": "sgn",
11+
"n_blocks": 8,
12+
"halo_size": [
13+
256,
14+
256,
15+
50
16+
],
17+
"component_list": [
18+
1
19+
],
20+
"crop_centers": [
21+
[
22+
1300,
23+
1538,
24+
1377
25+
],
26+
[
27+
1479,
28+
1118,
29+
1468
30+
],
31+
[
32+
1124,
33+
1128,
34+
1020
35+
],
36+
[
37+
620,
38+
1275,
39+
1326
40+
],
41+
[
42+
796,
43+
1019,
44+
1809
45+
],
46+
[
47+
1029,
48+
499,
49+
1628
50+
],
51+
[
52+
860,
53+
170,
54+
1115
55+
],
56+
[
57+
288,
58+
198,
59+
924
60+
]
61+
]
62+
}
63+
]
Lines changed: 27 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_R",
4+
"image_channel": [
5+
"GFP",
6+
"PV",
7+
"SGN_v2"
8+
],
9+
"segmentation_channel": "SGN_v2",
10+
"component_list": [
11+
2
12+
],
13+
"type": "sgn",
14+
"halo_size": [
15+
256,
16+
256,
17+
50
18+
],
19+
"crop_centers": [
20+
[
21+
645,
22+
435,
23+
815
24+
]
25+
]
26+
}
27+
]
Lines changed: 55 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
1+
[
2+
{
3+
"cochlea": "M_LR_000153_L",
4+
"image_channel": [
5+
"PV",
6+
"GFP",
7+
"SGN_v2"
8+
],
9+
"segmentation_channel": "SGN_v2",
10+
"type": "sgn",
11+
"n_blocks": 6,
12+
"halo_size": [
13+
256,
14+
256,
15+
50
16+
],
17+
"component_list": [
18+
1,
19+
2,
20+
3
21+
],
22+
"crop_centers": [
23+
[
24+
1225,
25+
638,
26+
807
27+
],
28+
[
29+
1310,
30+
378,
31+
878
32+
],
33+
[
34+
1152,
35+
239,
36+
1061
37+
],
38+
[
39+
860,
40+
186,
41+
1052
42+
],
43+
[
44+
830,
45+
297,
46+
692
47+
],
48+
[
49+
1073,
50+
325,
51+
448
52+
]
53+
]
54+
}
55+
]
Lines changed: 41 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,41 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000011_R",
4+
"image_channel": [
5+
"Myo7a_resized",
6+
"IHC_resized_v4b"
7+
],
8+
"segmentation_channel": "IHC_resized_v4b",
9+
"type": "ihc",
10+
"halo_size": [
11+
256,
12+
256,
13+
50
14+
],
15+
"component_list": [
16+
1
17+
],
18+
"crop_centers": [
19+
[
20+
1300,
21+
1780,
22+
1320
23+
],
24+
[
25+
1500,
26+
1270,
27+
1500
28+
],
29+
[
30+
1530,
31+
1440,
32+
540
33+
],
34+
[
35+
930,
36+
550,
37+
1940
38+
]
39+
]
40+
}
41+
]
Lines changed: 55 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
1+
[
2+
{
3+
"cochlea": "M_LR_000215_R",
4+
"image_channel": [
5+
"CR",
6+
"IHC_v4b"
7+
],
8+
"segmentation_channel": "IHC_v4b",
9+
"type": "ihc",
10+
"n_blocks": 6,
11+
"halo_size": [
12+
256,
13+
256,
14+
50
15+
],
16+
"component_list": [
17+
7,
18+
4,
19+
1,
20+
11
21+
],
22+
"crop_centers": [
23+
[
24+
464,
25+
1233,
26+
828
27+
],
28+
[
29+
1106,
30+
1007,
31+
821
32+
],
33+
[
34+
670,
35+
438,
36+
1048
37+
],
38+
[
39+
273,
40+
931,
41+
671
42+
],
43+
[
44+
934,
45+
937,
46+
293
47+
],
48+
[
49+
1167,
50+
259,
51+
591
52+
]
53+
]
54+
}
55+
]
Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_L",
4+
"image_channel": [
5+
"GFP"
6+
],
7+
"segmentation_channel": "SGN_v2",
8+
"background_mask": "yes",
9+
"component_list": [
10+
1,
11+
3,
12+
4,
13+
5
14+
]
15+
}
16+
]
Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,14 @@
1+
[
2+
{
3+
"cochlea": "G_EK_000049_R",
4+
"image_channel": [
5+
"GFP"
6+
],
7+
"segmentation_channel": "SGN_v2",
8+
"background_mask": "yes",
9+
"component_list": [
10+
1,
11+
2
12+
]
13+
}
14+
]

0 commit comments

Comments
 (0)