celldetective 1.3.0__py3-none-any.whl → 1.3.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- celldetective/_version.py +1 -1
- celldetective/events.py +86 -11
- celldetective/extra_properties.py +5 -1
- celldetective/gui/InitWindow.py +35 -9
- celldetective/gui/classifier_widget.py +57 -24
- celldetective/gui/layouts.py +128 -7
- celldetective/gui/measurement_options.py +3 -3
- celldetective/gui/process_block.py +46 -12
- celldetective/gui/retrain_segmentation_model_options.py +24 -10
- celldetective/gui/survival_ui.py +19 -2
- celldetective/gui/viewers.py +263 -3
- celldetective/io.py +4 -1
- celldetective/links/zenodo.json +136 -123
- celldetective/measure.py +5 -5
- celldetective/models/tracking_configs/biased_motion.json +68 -0
- celldetective/models/tracking_configs/no_z_motion.json +202 -0
- celldetective/preprocessing.py +172 -3
- celldetective/signals.py +5 -2
- celldetective/tracking.py +7 -3
- celldetective/utils.py +6 -6
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/METADATA +3 -3
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/RECORD +26 -24
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/WHEEL +1 -1
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/LICENSE +0 -0
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/entry_points.txt +0 -0
- {celldetective-1.3.0.dist-info → celldetective-1.3.1.dist-info}/top_level.txt +0 -0
celldetective/links/zenodo.json
CHANGED
|
@@ -8,9 +8,9 @@
|
|
|
8
8
|
"record": "public",
|
|
9
9
|
"status": "open"
|
|
10
10
|
},
|
|
11
|
-
"created": "2024-
|
|
11
|
+
"created": "2024-11-08T13:09:20.134692+00:00",
|
|
12
12
|
"custom_fields": {
|
|
13
|
-
"code:codeRepository": "https://github.com/
|
|
13
|
+
"code:codeRepository": "https://github.com/celldetective/celldetective",
|
|
14
14
|
"code:developmentStatus": {
|
|
15
15
|
"id": "active",
|
|
16
16
|
"title": {
|
|
@@ -41,11 +41,11 @@
|
|
|
41
41
|
},
|
|
42
42
|
"checksum": "md5:a88f2cbff39cab4369d80bfadbf31906",
|
|
43
43
|
"ext": "zip",
|
|
44
|
-
"id": "
|
|
44
|
+
"id": "e7d7f0c8-cb98-4b1d-ad9f-facf629934c7",
|
|
45
45
|
"key": "CP_cyto3.zip",
|
|
46
46
|
"links": {
|
|
47
|
-
"content": "https://zenodo.org/api/records/
|
|
48
|
-
"self": "https://zenodo.org/api/records/
|
|
47
|
+
"content": "https://zenodo.org/api/records/14055960/files/CP_cyto3.zip/content",
|
|
48
|
+
"self": "https://zenodo.org/api/records/14055960/files/CP_cyto3.zip"
|
|
49
49
|
},
|
|
50
50
|
"metadata": {},
|
|
51
51
|
"mimetype": "application/zip",
|
|
@@ -58,11 +58,11 @@
|
|
|
58
58
|
},
|
|
59
59
|
"checksum": "md5:4a158688881c68de0d14117db2880930",
|
|
60
60
|
"ext": "zip",
|
|
61
|
-
"id": "
|
|
61
|
+
"id": "e5b9d25f-1380-4c5a-b77b-ed166ad53eb3",
|
|
62
62
|
"key": "CP_livecell.zip",
|
|
63
63
|
"links": {
|
|
64
|
-
"content": "https://zenodo.org/api/records/
|
|
65
|
-
"self": "https://zenodo.org/api/records/
|
|
64
|
+
"content": "https://zenodo.org/api/records/14055960/files/CP_livecell.zip/content",
|
|
65
|
+
"self": "https://zenodo.org/api/records/14055960/files/CP_livecell.zip"
|
|
66
66
|
},
|
|
67
67
|
"metadata": {},
|
|
68
68
|
"mimetype": "application/zip",
|
|
@@ -75,11 +75,11 @@
|
|
|
75
75
|
},
|
|
76
76
|
"checksum": "md5:479209924265c41bd04d50341b51da04",
|
|
77
77
|
"ext": "zip",
|
|
78
|
-
"id": "
|
|
78
|
+
"id": "65198f8c-6e62-44f3-831c-68069f003c90",
|
|
79
79
|
"key": "CP_nuclei.zip",
|
|
80
80
|
"links": {
|
|
81
|
-
"content": "https://zenodo.org/api/records/
|
|
82
|
-
"self": "https://zenodo.org/api/records/
|
|
81
|
+
"content": "https://zenodo.org/api/records/14055960/files/CP_nuclei.zip/content",
|
|
82
|
+
"self": "https://zenodo.org/api/records/14055960/files/CP_nuclei.zip"
|
|
83
83
|
},
|
|
84
84
|
"metadata": {},
|
|
85
85
|
"mimetype": "application/zip",
|
|
@@ -92,11 +92,11 @@
|
|
|
92
92
|
},
|
|
93
93
|
"checksum": "md5:ea161f28b6159c492c7fa8a76970017c",
|
|
94
94
|
"ext": "zip",
|
|
95
|
-
"id": "
|
|
95
|
+
"id": "9e379125-86b0-444a-972a-abbb5d07ad5f",
|
|
96
96
|
"key": "CP_tissuenet.zip",
|
|
97
97
|
"links": {
|
|
98
|
-
"content": "https://zenodo.org/api/records/
|
|
99
|
-
"self": "https://zenodo.org/api/records/
|
|
98
|
+
"content": "https://zenodo.org/api/records/14055960/files/CP_tissuenet.zip/content",
|
|
99
|
+
"self": "https://zenodo.org/api/records/14055960/files/CP_tissuenet.zip"
|
|
100
100
|
},
|
|
101
101
|
"metadata": {},
|
|
102
102
|
"mimetype": "application/zip",
|
|
@@ -109,11 +109,11 @@
|
|
|
109
109
|
},
|
|
110
110
|
"checksum": "md5:673951a63ad0ea0fbfa443cfa78b0102",
|
|
111
111
|
"ext": "zip",
|
|
112
|
-
"id": "
|
|
112
|
+
"id": "28067cad-0e6a-4ab7-8981-2b793dbfcb39",
|
|
113
113
|
"key": "NucCond.zip",
|
|
114
114
|
"links": {
|
|
115
|
-
"content": "https://zenodo.org/api/records/
|
|
116
|
-
"self": "https://zenodo.org/api/records/
|
|
115
|
+
"content": "https://zenodo.org/api/records/14055960/files/NucCond.zip/content",
|
|
116
|
+
"self": "https://zenodo.org/api/records/14055960/files/NucCond.zip"
|
|
117
117
|
},
|
|
118
118
|
"metadata": {},
|
|
119
119
|
"mimetype": "application/zip",
|
|
@@ -126,11 +126,11 @@
|
|
|
126
126
|
},
|
|
127
127
|
"checksum": "md5:49592e9f05a796d2787652e36c8ef6e2",
|
|
128
128
|
"ext": "zip",
|
|
129
|
-
"id": "
|
|
129
|
+
"id": "ca3dcb1f-d740-4df4-bcdd-bfd91ff8ffe0",
|
|
130
130
|
"key": "SD_versatile_fluo.zip",
|
|
131
131
|
"links": {
|
|
132
|
-
"content": "https://zenodo.org/api/records/
|
|
133
|
-
"self": "https://zenodo.org/api/records/
|
|
132
|
+
"content": "https://zenodo.org/api/records/14055960/files/SD_versatile_fluo.zip/content",
|
|
133
|
+
"self": "https://zenodo.org/api/records/14055960/files/SD_versatile_fluo.zip"
|
|
134
134
|
},
|
|
135
135
|
"metadata": {},
|
|
136
136
|
"mimetype": "application/zip",
|
|
@@ -143,11 +143,11 @@
|
|
|
143
143
|
},
|
|
144
144
|
"checksum": "md5:186bf4be5f78763dde9b181aa8f8d116",
|
|
145
145
|
"ext": "zip",
|
|
146
|
-
"id": "
|
|
146
|
+
"id": "e70ea001-96da-4649-a325-e5ff310e00de",
|
|
147
147
|
"key": "SD_versatile_he.zip",
|
|
148
148
|
"links": {
|
|
149
|
-
"content": "https://zenodo.org/api/records/
|
|
150
|
-
"self": "https://zenodo.org/api/records/
|
|
149
|
+
"content": "https://zenodo.org/api/records/14055960/files/SD_versatile_he.zip/content",
|
|
150
|
+
"self": "https://zenodo.org/api/records/14055960/files/SD_versatile_he.zip"
|
|
151
151
|
},
|
|
152
152
|
"metadata": {},
|
|
153
153
|
"mimetype": "application/zip",
|
|
@@ -158,85 +158,85 @@
|
|
|
158
158
|
"access": {
|
|
159
159
|
"hidden": false
|
|
160
160
|
},
|
|
161
|
-
"checksum": "md5:
|
|
161
|
+
"checksum": "md5:0e2d912b6241446120b446b4a412218d",
|
|
162
162
|
"ext": "zip",
|
|
163
|
-
"id": "
|
|
163
|
+
"id": "8332f59e-b71b-4af0-81b2-0c391ce9356d",
|
|
164
164
|
"key": "db-si-NucCondensation.zip",
|
|
165
165
|
"links": {
|
|
166
|
-
"content": "https://zenodo.org/api/records/
|
|
167
|
-
"self": "https://zenodo.org/api/records/
|
|
166
|
+
"content": "https://zenodo.org/api/records/14055960/files/db-si-NucCondensation.zip/content",
|
|
167
|
+
"self": "https://zenodo.org/api/records/14055960/files/db-si-NucCondensation.zip"
|
|
168
168
|
},
|
|
169
169
|
"metadata": {},
|
|
170
170
|
"mimetype": "application/zip",
|
|
171
|
-
"size":
|
|
171
|
+
"size": 19184687,
|
|
172
172
|
"storage_class": "L"
|
|
173
173
|
},
|
|
174
174
|
"db-si-NucPI.zip": {
|
|
175
175
|
"access": {
|
|
176
176
|
"hidden": false
|
|
177
177
|
},
|
|
178
|
-
"checksum": "md5:
|
|
178
|
+
"checksum": "md5:24d6da6c42435fdd0fa6a87616033b7c",
|
|
179
179
|
"ext": "zip",
|
|
180
|
-
"id": "
|
|
180
|
+
"id": "e332de75-5583-4517-b60b-a69438a88d11",
|
|
181
181
|
"key": "db-si-NucPI.zip",
|
|
182
182
|
"links": {
|
|
183
|
-
"content": "https://zenodo.org/api/records/
|
|
184
|
-
"self": "https://zenodo.org/api/records/
|
|
183
|
+
"content": "https://zenodo.org/api/records/14055960/files/db-si-NucPI.zip/content",
|
|
184
|
+
"self": "https://zenodo.org/api/records/14055960/files/db-si-NucPI.zip"
|
|
185
185
|
},
|
|
186
186
|
"metadata": {},
|
|
187
187
|
"mimetype": "application/zip",
|
|
188
|
-
"size":
|
|
188
|
+
"size": 30359292,
|
|
189
189
|
"storage_class": "L"
|
|
190
190
|
},
|
|
191
191
|
"db_mcf7_nuclei_w_lymphocytes.zip": {
|
|
192
192
|
"access": {
|
|
193
193
|
"hidden": false
|
|
194
194
|
},
|
|
195
|
-
"checksum": "md5:
|
|
195
|
+
"checksum": "md5:d893ef8c69133ad3bb076adaef8aaf8d",
|
|
196
196
|
"ext": "zip",
|
|
197
|
-
"id": "
|
|
197
|
+
"id": "c9468f12-60a5-49ae-8979-9438acbea90d",
|
|
198
198
|
"key": "db_mcf7_nuclei_w_lymphocytes.zip",
|
|
199
199
|
"links": {
|
|
200
|
-
"content": "https://zenodo.org/api/records/
|
|
201
|
-
"self": "https://zenodo.org/api/records/
|
|
200
|
+
"content": "https://zenodo.org/api/records/14055960/files/db_mcf7_nuclei_w_lymphocytes.zip/content",
|
|
201
|
+
"self": "https://zenodo.org/api/records/14055960/files/db_mcf7_nuclei_w_lymphocytes.zip"
|
|
202
202
|
},
|
|
203
203
|
"metadata": {},
|
|
204
204
|
"mimetype": "application/zip",
|
|
205
|
-
"size":
|
|
205
|
+
"size": 336641891,
|
|
206
206
|
"storage_class": "L"
|
|
207
207
|
},
|
|
208
208
|
"db_primary_NK_w_mcf7.zip": {
|
|
209
209
|
"access": {
|
|
210
210
|
"hidden": false
|
|
211
211
|
},
|
|
212
|
-
"checksum": "md5:
|
|
212
|
+
"checksum": "md5:d0ae0d92264523bf69ea76865839fce1",
|
|
213
213
|
"ext": "zip",
|
|
214
|
-
"id": "
|
|
214
|
+
"id": "221a922f-80d4-4de1-a80e-0f871f06957f",
|
|
215
215
|
"key": "db_primary_NK_w_mcf7.zip",
|
|
216
216
|
"links": {
|
|
217
|
-
"content": "https://zenodo.org/api/records/
|
|
218
|
-
"self": "https://zenodo.org/api/records/
|
|
217
|
+
"content": "https://zenodo.org/api/records/14055960/files/db_primary_NK_w_mcf7.zip/content",
|
|
218
|
+
"self": "https://zenodo.org/api/records/14055960/files/db_primary_NK_w_mcf7.zip"
|
|
219
219
|
},
|
|
220
220
|
"metadata": {},
|
|
221
221
|
"mimetype": "application/zip",
|
|
222
|
-
"size":
|
|
222
|
+
"size": 629359485,
|
|
223
223
|
"storage_class": "L"
|
|
224
224
|
},
|
|
225
225
|
"db_spreading_lymphocytes.zip": {
|
|
226
226
|
"access": {
|
|
227
227
|
"hidden": false
|
|
228
228
|
},
|
|
229
|
-
"checksum": "md5:
|
|
229
|
+
"checksum": "md5:fb3eb4a57275507a9fd505e8c0bf3587",
|
|
230
230
|
"ext": "zip",
|
|
231
|
-
"id": "
|
|
231
|
+
"id": "76db95ae-1ebc-401a-a538-fb099f0fa65c",
|
|
232
232
|
"key": "db_spreading_lymphocytes.zip",
|
|
233
233
|
"links": {
|
|
234
|
-
"content": "https://zenodo.org/api/records/
|
|
235
|
-
"self": "https://zenodo.org/api/records/
|
|
234
|
+
"content": "https://zenodo.org/api/records/14055960/files/db_spreading_lymphocytes.zip/content",
|
|
235
|
+
"self": "https://zenodo.org/api/records/14055960/files/db_spreading_lymphocytes.zip"
|
|
236
236
|
},
|
|
237
237
|
"metadata": {},
|
|
238
238
|
"mimetype": "application/zip",
|
|
239
|
-
"size":
|
|
239
|
+
"size": 509933296,
|
|
240
240
|
"storage_class": "L"
|
|
241
241
|
},
|
|
242
242
|
"demo_adcc.zip": {
|
|
@@ -245,11 +245,11 @@
|
|
|
245
245
|
},
|
|
246
246
|
"checksum": "md5:3a826e2f02c42a8fc66344c27891539e",
|
|
247
247
|
"ext": "zip",
|
|
248
|
-
"id": "
|
|
248
|
+
"id": "8528d27a-f851-4ff9-a9ea-0caefd862900",
|
|
249
249
|
"key": "demo_adcc.zip",
|
|
250
250
|
"links": {
|
|
251
|
-
"content": "https://zenodo.org/api/records/
|
|
252
|
-
"self": "https://zenodo.org/api/records/
|
|
251
|
+
"content": "https://zenodo.org/api/records/14055960/files/demo_adcc.zip/content",
|
|
252
|
+
"self": "https://zenodo.org/api/records/14055960/files/demo_adcc.zip"
|
|
253
253
|
},
|
|
254
254
|
"metadata": {},
|
|
255
255
|
"mimetype": "application/zip",
|
|
@@ -262,11 +262,11 @@
|
|
|
262
262
|
},
|
|
263
263
|
"checksum": "md5:21152b506b4b9b54a15c7c5c6e25df36",
|
|
264
264
|
"ext": "zip",
|
|
265
|
-
"id": "
|
|
265
|
+
"id": "6d06ee77-7d56-434d-ba15-874b6773b3ef",
|
|
266
266
|
"key": "demo_ricm.zip",
|
|
267
267
|
"links": {
|
|
268
|
-
"content": "https://zenodo.org/api/records/
|
|
269
|
-
"self": "https://zenodo.org/api/records/
|
|
268
|
+
"content": "https://zenodo.org/api/records/14055960/files/demo_ricm.zip/content",
|
|
269
|
+
"self": "https://zenodo.org/api/records/14055960/files/demo_ricm.zip"
|
|
270
270
|
},
|
|
271
271
|
"metadata": {},
|
|
272
272
|
"mimetype": "application/zip",
|
|
@@ -279,11 +279,11 @@
|
|
|
279
279
|
},
|
|
280
280
|
"checksum": "md5:d727d15d18225a76ac2944be2c29a538",
|
|
281
281
|
"ext": "zip",
|
|
282
|
-
"id": "
|
|
282
|
+
"id": "e154d694-c796-4924-8b38-68ba613c7a05",
|
|
283
283
|
"key": "lymphocytes_ricm.zip",
|
|
284
284
|
"links": {
|
|
285
|
-
"content": "https://zenodo.org/api/records/
|
|
286
|
-
"self": "https://zenodo.org/api/records/
|
|
285
|
+
"content": "https://zenodo.org/api/records/14055960/files/lymphocytes_ricm.zip/content",
|
|
286
|
+
"self": "https://zenodo.org/api/records/14055960/files/lymphocytes_ricm.zip"
|
|
287
287
|
},
|
|
288
288
|
"metadata": {},
|
|
289
289
|
"mimetype": "application/zip",
|
|
@@ -296,11 +296,11 @@
|
|
|
296
296
|
},
|
|
297
297
|
"checksum": "md5:f8553e793c70b64ebc7b4e4720dcde89",
|
|
298
298
|
"ext": "zip",
|
|
299
|
-
"id": "
|
|
299
|
+
"id": "a73fe93c-2fa4-492f-bf94-9a0afb134e4d",
|
|
300
300
|
"key": "lysis_H_PI.zip",
|
|
301
301
|
"links": {
|
|
302
|
-
"content": "https://zenodo.org/api/records/
|
|
303
|
-
"self": "https://zenodo.org/api/records/
|
|
302
|
+
"content": "https://zenodo.org/api/records/14055960/files/lysis_H_PI.zip/content",
|
|
303
|
+
"self": "https://zenodo.org/api/records/14055960/files/lysis_H_PI.zip"
|
|
304
304
|
},
|
|
305
305
|
"metadata": {},
|
|
306
306
|
"mimetype": "application/zip",
|
|
@@ -311,17 +311,17 @@
|
|
|
311
311
|
"access": {
|
|
312
312
|
"hidden": false
|
|
313
313
|
},
|
|
314
|
-
"checksum": "md5:
|
|
314
|
+
"checksum": "md5:17f078d0b1ab4be198709d79948da46c",
|
|
315
315
|
"ext": "zip",
|
|
316
|
-
"id": "
|
|
316
|
+
"id": "4867138a-7a35-4ac3-926f-675a842fa084",
|
|
317
317
|
"key": "lysis_PI_area.zip",
|
|
318
318
|
"links": {
|
|
319
|
-
"content": "https://zenodo.org/api/records/
|
|
320
|
-
"self": "https://zenodo.org/api/records/
|
|
319
|
+
"content": "https://zenodo.org/api/records/14055960/files/lysis_PI_area.zip/content",
|
|
320
|
+
"self": "https://zenodo.org/api/records/14055960/files/lysis_PI_area.zip"
|
|
321
321
|
},
|
|
322
322
|
"metadata": {},
|
|
323
323
|
"mimetype": "application/zip",
|
|
324
|
-
"size":
|
|
324
|
+
"size": 33964442,
|
|
325
325
|
"storage_class": "L"
|
|
326
326
|
},
|
|
327
327
|
"mcf7_nuc_multimodal.zip": {
|
|
@@ -330,11 +330,11 @@
|
|
|
330
330
|
},
|
|
331
331
|
"checksum": "md5:0feb3dd50573f432dc441429e32158f1",
|
|
332
332
|
"ext": "zip",
|
|
333
|
-
"id": "
|
|
333
|
+
"id": "5eb661b1-d393-4fb3-a7a8-9aeb901666b5",
|
|
334
334
|
"key": "mcf7_nuc_multimodal.zip",
|
|
335
335
|
"links": {
|
|
336
|
-
"content": "https://zenodo.org/api/records/
|
|
337
|
-
"self": "https://zenodo.org/api/records/
|
|
336
|
+
"content": "https://zenodo.org/api/records/14055960/files/mcf7_nuc_multimodal.zip/content",
|
|
337
|
+
"self": "https://zenodo.org/api/records/14055960/files/mcf7_nuc_multimodal.zip"
|
|
338
338
|
},
|
|
339
339
|
"metadata": {},
|
|
340
340
|
"mimetype": "application/zip",
|
|
@@ -347,11 +347,11 @@
|
|
|
347
347
|
},
|
|
348
348
|
"checksum": "md5:f263d38dd8a6b3095ac594ca044ee3e8",
|
|
349
349
|
"ext": "zip",
|
|
350
|
-
"id": "
|
|
350
|
+
"id": "2aed0230-eceb-44d4-aced-ca58295998f4",
|
|
351
351
|
"key": "mcf7_nuc_stardist_transfer.zip",
|
|
352
352
|
"links": {
|
|
353
|
-
"content": "https://zenodo.org/api/records/
|
|
354
|
-
"self": "https://zenodo.org/api/records/
|
|
353
|
+
"content": "https://zenodo.org/api/records/14055960/files/mcf7_nuc_stardist_transfer.zip/content",
|
|
354
|
+
"self": "https://zenodo.org/api/records/14055960/files/mcf7_nuc_stardist_transfer.zip"
|
|
355
355
|
},
|
|
356
356
|
"metadata": {},
|
|
357
357
|
"mimetype": "application/zip",
|
|
@@ -362,70 +362,72 @@
|
|
|
362
362
|
"access": {
|
|
363
363
|
"hidden": false
|
|
364
364
|
},
|
|
365
|
-
"checksum": "md5:
|
|
365
|
+
"checksum": "md5:1a907cf702a2d0fb04dd8f22f39c7705",
|
|
366
366
|
"ext": "zip",
|
|
367
|
-
"id": "
|
|
367
|
+
"id": "e2b9aca3-cd3d-4985-bed5-609e936fc5d9",
|
|
368
368
|
"key": "primNK_cfse.zip",
|
|
369
369
|
"links": {
|
|
370
|
-
"content": "https://zenodo.org/api/records/
|
|
371
|
-
"self": "https://zenodo.org/api/records/
|
|
370
|
+
"content": "https://zenodo.org/api/records/14055960/files/primNK_cfse.zip/content",
|
|
371
|
+
"self": "https://zenodo.org/api/records/14055960/files/primNK_cfse.zip"
|
|
372
372
|
},
|
|
373
373
|
"metadata": {},
|
|
374
374
|
"mimetype": "application/zip",
|
|
375
|
-
"size":
|
|
375
|
+
"size": 24582160,
|
|
376
376
|
"storage_class": "L"
|
|
377
377
|
},
|
|
378
378
|
"primNK_multimodal.zip": {
|
|
379
379
|
"access": {
|
|
380
380
|
"hidden": false
|
|
381
381
|
},
|
|
382
|
-
"checksum": "md5:
|
|
382
|
+
"checksum": "md5:f127dbba4988ad6b746b860a6efdcdea",
|
|
383
383
|
"ext": "zip",
|
|
384
|
-
"id": "
|
|
384
|
+
"id": "54edce4a-3763-4ee2-accc-c1dc412697e5",
|
|
385
385
|
"key": "primNK_multimodal.zip",
|
|
386
386
|
"links": {
|
|
387
|
-
"content": "https://zenodo.org/api/records/
|
|
388
|
-
"self": "https://zenodo.org/api/records/
|
|
387
|
+
"content": "https://zenodo.org/api/records/14055960/files/primNK_multimodal.zip/content",
|
|
388
|
+
"self": "https://zenodo.org/api/records/14055960/files/primNK_multimodal.zip"
|
|
389
389
|
},
|
|
390
390
|
"metadata": {},
|
|
391
391
|
"mimetype": "application/zip",
|
|
392
|
-
"size":
|
|
392
|
+
"size": 24346373,
|
|
393
393
|
"storage_class": "L"
|
|
394
394
|
}
|
|
395
395
|
},
|
|
396
396
|
"order": [],
|
|
397
|
-
"total_bytes":
|
|
397
|
+
"total_bytes": 3068558166
|
|
398
398
|
},
|
|
399
|
-
"id": "
|
|
399
|
+
"id": "14055960",
|
|
400
400
|
"is_draft": false,
|
|
401
401
|
"is_published": true,
|
|
402
402
|
"links": {
|
|
403
|
-
"access": "https://zenodo.org/api/records/
|
|
404
|
-
"access_grants": "https://zenodo.org/api/records/
|
|
405
|
-
"access_links": "https://zenodo.org/api/records/
|
|
406
|
-
"access_request": "https://zenodo.org/api/records/
|
|
407
|
-
"access_users": "https://zenodo.org/api/records/
|
|
408
|
-
"archive": "https://zenodo.org/api/records/
|
|
409
|
-
"archive_media": "https://zenodo.org/api/records/
|
|
410
|
-
"communities": "https://zenodo.org/api/records/
|
|
411
|
-
"communities-suggestions": "https://zenodo.org/api/records/
|
|
412
|
-
"doi": "https://doi.org/10.5281/zenodo.
|
|
413
|
-
"draft": "https://zenodo.org/api/records/
|
|
414
|
-
"files": "https://zenodo.org/api/records/
|
|
415
|
-
"latest": "https://zenodo.org/api/records/
|
|
416
|
-
"latest_html": "https://zenodo.org/records/
|
|
417
|
-
"media_files": "https://zenodo.org/api/records/
|
|
403
|
+
"access": "https://zenodo.org/api/records/14055960/access",
|
|
404
|
+
"access_grants": "https://zenodo.org/api/records/14055960/access/grants",
|
|
405
|
+
"access_links": "https://zenodo.org/api/records/14055960/access/links",
|
|
406
|
+
"access_request": "https://zenodo.org/api/records/14055960/access/request",
|
|
407
|
+
"access_users": "https://zenodo.org/api/records/14055960/access/users",
|
|
408
|
+
"archive": "https://zenodo.org/api/records/14055960/files-archive",
|
|
409
|
+
"archive_media": "https://zenodo.org/api/records/14055960/media-files-archive",
|
|
410
|
+
"communities": "https://zenodo.org/api/records/14055960/communities",
|
|
411
|
+
"communities-suggestions": "https://zenodo.org/api/records/14055960/communities-suggestions",
|
|
412
|
+
"doi": "https://doi.org/10.5281/zenodo.14055960",
|
|
413
|
+
"draft": "https://zenodo.org/api/records/14055960/draft",
|
|
414
|
+
"files": "https://zenodo.org/api/records/14055960/files",
|
|
415
|
+
"latest": "https://zenodo.org/api/records/14055960/versions/latest",
|
|
416
|
+
"latest_html": "https://zenodo.org/records/14055960/latest",
|
|
417
|
+
"media_files": "https://zenodo.org/api/records/14055960/media-files",
|
|
418
418
|
"parent": "https://zenodo.org/api/records/10650278",
|
|
419
|
-
"parent_doi": "https://
|
|
419
|
+
"parent_doi": "https://doi.org/10.5281/zenodo.10650278",
|
|
420
|
+
"parent_doi_html": "https://zenodo.org/doi/10.5281/zenodo.10650278",
|
|
420
421
|
"parent_html": "https://zenodo.org/records/10650278",
|
|
421
|
-
"requests": "https://zenodo.org/api/records/
|
|
422
|
-
"reserve_doi": "https://zenodo.org/api/records/
|
|
423
|
-
"self": "https://zenodo.org/api/records/
|
|
424
|
-
"self_doi": "https://
|
|
425
|
-
"
|
|
426
|
-
"
|
|
427
|
-
"
|
|
428
|
-
"
|
|
422
|
+
"requests": "https://zenodo.org/api/records/14055960/requests",
|
|
423
|
+
"reserve_doi": "https://zenodo.org/api/records/14055960/draft/pids/doi",
|
|
424
|
+
"self": "https://zenodo.org/api/records/14055960",
|
|
425
|
+
"self_doi": "https://doi.org/10.5281/zenodo.14055960",
|
|
426
|
+
"self_doi_html": "https://zenodo.org/doi/10.5281/zenodo.14055960",
|
|
427
|
+
"self_html": "https://zenodo.org/records/14055960",
|
|
428
|
+
"self_iiif_manifest": "https://zenodo.org/api/iiif/record:14055960/manifest",
|
|
429
|
+
"self_iiif_sequence": "https://zenodo.org/api/iiif/record:14055960/sequence/default",
|
|
430
|
+
"versions": "https://zenodo.org/api/records/14055960/versions"
|
|
429
431
|
},
|
|
430
432
|
"media_files": {
|
|
431
433
|
"count": 0,
|
|
@@ -577,11 +579,10 @@
|
|
|
577
579
|
"type": "personal"
|
|
578
580
|
},
|
|
579
581
|
"role": {
|
|
580
|
-
"id": "
|
|
582
|
+
"id": "projectmember",
|
|
581
583
|
"title": {
|
|
582
|
-
"de": "
|
|
583
|
-
"en": "
|
|
584
|
-
"sv": "Annotator"
|
|
584
|
+
"de": "Projektmitglied",
|
|
585
|
+
"en": "Project member"
|
|
585
586
|
}
|
|
586
587
|
}
|
|
587
588
|
},
|
|
@@ -661,8 +662,20 @@
|
|
|
661
662
|
}
|
|
662
663
|
}
|
|
663
664
|
],
|
|
664
|
-
"
|
|
665
|
-
|
|
665
|
+
"dates": [
|
|
666
|
+
{
|
|
667
|
+
"date": "2024-11-08",
|
|
668
|
+
"type": {
|
|
669
|
+
"id": "available",
|
|
670
|
+
"title": {
|
|
671
|
+
"de": "Verf\u00fcgbar",
|
|
672
|
+
"en": "Available"
|
|
673
|
+
}
|
|
674
|
+
}
|
|
675
|
+
}
|
|
676
|
+
],
|
|
677
|
+
"description": "<p>This repository contains datasets, models and demos associated to <a href=\"https://github.com/remyeltorro/celldetective\">Celldetective</a>, a software for single-cell analysis from multimodal time lapse microscopy images. </p>\n<h1>Demos</h1>\n<h2>Cell-cell interaction assay: ADCC</h2>\n<p>We imaged a co-culture of MCF-7 breast cancer cells (targets) and human primary NK cells (effectors), interacting in the presence of bispecific antibodies, to measure antibody dependent cellular cytotoxicity (ADCC). The nuclei of all cells are marked with the Hoechst nuclear stain, the dead nuclei with the propidium iodide nuclear stain, the cytoplasm of the NK cells with CFSE. The system in epifluorescence and brightfield at either 20 or 40X magnification. We provide a single position demo for the ADCC assay, as \"demo_adcc.zip\". After unzipping, the demo_adcc folder can be loaded in Celldetective for testing. </p>\n<h2>Cell-surface interaction assay: RICM</h2>\n<p>We imaged human primary NK cells engaging in spreading with a surface coated with a bispecific antibody similar to the one used in the ADCC assay (replacing the target cells with a flat surface). The system is imaged using the RICM technique. Images are normalized using a median estimate of the background, pooled from all the positions in a well and dividing the images by this estimate. Here, we provide a single position demo for the cell-surface interactiona assay imaged in RICM, as \"demo_ricm.zip\". As above, after unzipping, the experiment can be tested and processed in Celldetective.</p>\n<h1>Datasets</h1>\n<h2>Image annotations for segmentation</h2>\n<h3>Cell-cell interaction assay: ADCC</h3>\n<p>We generated two sets of annotations from images of a co-culture of MCF-7 breast cancer cells and human primary NK cells, interacting in the presence of bispecific antibodies, to measure antibody dependent cellular cytotoxicity (ADCC). Since there are two separate cell populations of interest, the targets (MCF-7) and effectors (NK cells), we curated two datasets. Each sample in a dataset consists of a multichannel image (up to five channels in the context of ADCC, among brightfield , Hoechst nuclear stain, PI nuclear stain, CFSE, LAMP1), the associated instance segmentation annotation for the population of interest and a json file summarizing the content of each channel and the spatial calibration of the image. These sample data are generated directly in Celldetective, using a custom napari plugin.</p>\n<ul>\n<li>db_mcf7_nuclei_w_lymphocytes: MCF-7 cell nuclei are annotated specifically on images where primary NK cells (or rarely primary T cells), and RBCs co-exist. The annotation exploits up to four channels simultaneously.</li>\n<li>db_primary_NK_w_mcf7: human primary NK cells, with annotated cytoplasm (mostly from CFSE) but exploiting brightfield and Hoechst to segment out of focus or poorly labelled cells.</li>\n</ul>\n<p>These datasets are used to train several segmentation models to segment on one hand the MCF-7 nuclei and on the other hand the primary NK cells.</p>\n<h3>Cell-surface interaction assay: RICM</h3>\n<ul>\n<li>db_spreading_lymphocytes: we provide a dataset of primary NK cells (and occasionnaly mice T cells) imaged in RICM (with sometimes paired brightfield images). Cells are detected as soon as they start forming interferences on the image (hovering behavior). A pre-annotation was performed using a threshold based segmentation on the RICM modality. Manuel separation of cell-cell contacts and removal of false positive objects was performed by an expert annotator (using brightfield when available). RBCs are ignored in the annotations. </li>\n</ul>\n<h2>Single-cell signal annotations for classification and regression</h2>\n<h3>Cell-cell interaction assay: ADCC</h3>\n<p>We generated several signal classification/regression datasets with Celldetective to characterize the ADCC assay. Briefly, for a given event cells can be classified as \"the event occured during the observation\", \"no event occured during the observation\", \"the event already occured prior to observation\". If the event occurred during the observation, we can estimate when (the regression). Each single-cell is a dictionary with a collection of signals. The attribute \"class\" sets the class and \"t0\" the time of event (default is -1 for absence of event). </p>\n<ul>\n<li>db-si-NucPI: classification and regression of single-cells with respect to lysis events characterized by a strong PI increase upon lysis (also associated with decreasing nuclear area and sometimes a decreasing Hoechst)</li>\n<li>db-si-NucCondensation: classification and regression of single-cells with respect to nucleus shrinking events characterized by a decreasing nuclear area</li>\n</ul>\n<h1>Models</h1>\n<h2>Segmentation models</h2>\n<h3>Generalist models</h3>\n<p>We integrated in Celldetective select published models for cellular segmentation from StarDist and Cellpose. We wraped the models with an input configuration to help Celldetective handle the normalization, rescaling and channel selection upon inference. </p>\n<ul>\n<li>Cellpose [1,2]: <em>cyto3</em>, <em>livecell</em>, <em>tissuenet</em>, <em>nuclei</em></li>\n<li>StarDist [3]: <em>versatile_fluo</em>, <em>versatile_he</em></li>\n</ul>\n<p>If you use any of these models your research, don't forget to cite the StarDist or Cellpose papers accordingly!</p>\n<h3>ADCC models</h3>\n<ul>\n<li>MCF-7 (in the presence of lymphocytes): <em>mcf7_nuc_multimodal, mcf7_nuc_stardist_transfer</em></li>\n<li>primary NKs (in the presence of MCF-7): <em>primNK_multimodal</em>, <em>primNK_SD</em>, <em>primNK_cfse</em></li>\n</ul>\n<h3>Spreading-assay models</h3>\n<ul>\n<li>Lymphocytes: <em>lymphocytes_ricm</em></li>\n</ul>\n<h2>Signal analysis models</h2>\n<p>We developed Deep Learning models that classify and regress the time of events from single-cell signals, applied to the ADCC assay.</p>\n<ul>\n<li> lysis detection: <em>lysis_H_PI</em>, <em>lysis_PI_area</em>,<em>. </em>Detect lysis events characterized at least by an increase of PI from one or more measurements (respectively PI+Hoechst and PI+nucleus area, trained on db-si-NucPI)</li>\n<li>nucleus shrinking detection:<em> NucCond</em>. Detect nucleus shrinking events from nuclear area signal (db-si-NucCondensation)</li>\n</ul>\n<h1>References</h1>\n<ol>\n<li>Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021).</li>\n<li>Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat Methods 19, 1634–1641 (2022).</li>\n<li>Schmidt, U., Weigert, M., Broaddus, C. & Myers, G. Cell Detection with Star-Convex Polygons. in Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 (eds. Frangi, A. F., Schnabel, J. A., Davatzikos, C., Alberola-López, C. & Fichtinger, G.) 265–273 (Springer International Publishing, Cham, 2018). doi:10.1007/978-3-030-00934-2_30.</li>\n</ol>\n<p> </p>\n<p> </p>",
|
|
678
|
+
"publication_date": "2024-11-08",
|
|
666
679
|
"publisher": "Zenodo",
|
|
667
680
|
"resource_type": {
|
|
668
681
|
"id": "dataset",
|
|
@@ -688,7 +701,7 @@
|
|
|
688
701
|
}
|
|
689
702
|
],
|
|
690
703
|
"title": "Datasets, models and demos associated to \"Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions\"",
|
|
691
|
-
"version": "1.1.0"
|
|
704
|
+
"version": "1.1.0.post2"
|
|
692
705
|
},
|
|
693
706
|
"parent": {
|
|
694
707
|
"access": {
|
|
@@ -717,22 +730,22 @@
|
|
|
717
730
|
"pids": {
|
|
718
731
|
"doi": {
|
|
719
732
|
"client": "datacite",
|
|
720
|
-
"identifier": "10.5281/zenodo.
|
|
733
|
+
"identifier": "10.5281/zenodo.14055960",
|
|
721
734
|
"provider": "datacite"
|
|
722
735
|
},
|
|
723
736
|
"oai": {
|
|
724
|
-
"identifier": "oai:zenodo.org:
|
|
737
|
+
"identifier": "oai:zenodo.org:14055960",
|
|
725
738
|
"provider": "oai"
|
|
726
739
|
}
|
|
727
740
|
},
|
|
728
741
|
"revision_id": 4,
|
|
729
742
|
"stats": {
|
|
730
743
|
"all_versions": {
|
|
731
|
-
"data_volume":
|
|
732
|
-
"downloads":
|
|
733
|
-
"unique_downloads":
|
|
734
|
-
"unique_views":
|
|
735
|
-
"views":
|
|
744
|
+
"data_volume": 307526747054.0,
|
|
745
|
+
"downloads": 3921,
|
|
746
|
+
"unique_downloads": 3707,
|
|
747
|
+
"unique_views": 269,
|
|
748
|
+
"views": 295
|
|
736
749
|
},
|
|
737
750
|
"this_version": {
|
|
738
751
|
"data_volume": 0.0,
|
|
@@ -743,9 +756,9 @@
|
|
|
743
756
|
}
|
|
744
757
|
},
|
|
745
758
|
"status": "published",
|
|
746
|
-
"updated": "2024-
|
|
759
|
+
"updated": "2024-11-08T13:09:20.934553+00:00",
|
|
747
760
|
"versions": {
|
|
748
|
-
"index":
|
|
761
|
+
"index": 4,
|
|
749
762
|
"is_latest": true,
|
|
750
763
|
"is_latest_draft": true
|
|
751
764
|
}
|
celldetective/measure.py
CHANGED
|
@@ -1338,10 +1338,11 @@ def classify_cells_from_query(df, status_attr, query):
|
|
|
1338
1338
|
if not status_attr.startswith('status_'):
|
|
1339
1339
|
status_attr = 'status_'+status_attr
|
|
1340
1340
|
|
|
1341
|
-
df
|
|
1341
|
+
df = df.copy()
|
|
1342
|
+
df.loc[:,status_attr] = 0
|
|
1343
|
+
|
|
1342
1344
|
cols = extract_cols_from_query(query)
|
|
1343
1345
|
cols_in_df = np.all([c in list(df.columns) for c in cols], axis=0)
|
|
1344
|
-
|
|
1345
1346
|
if query=='':
|
|
1346
1347
|
print('The provided query is empty...')
|
|
1347
1348
|
else:
|
|
@@ -1354,11 +1355,10 @@ def classify_cells_from_query(df, status_attr, query):
|
|
|
1354
1355
|
df.loc[selection, status_attr] = 1
|
|
1355
1356
|
else:
|
|
1356
1357
|
df.loc[:, status_attr] = np.nan
|
|
1357
|
-
|
|
1358
1358
|
except Exception as e:
|
|
1359
|
-
print("The query could not be understood. No filtering was applied. {e}...")
|
|
1359
|
+
print(f"The query could not be understood. No filtering was applied. {e}...")
|
|
1360
1360
|
return None
|
|
1361
|
-
return df
|
|
1361
|
+
return df.copy()
|
|
1362
1362
|
|
|
1363
1363
|
def classify_tracks_from_query(df, event_name, query, irreversible_event=True, unique_state=False, r2_threshold=0.5, percentile_recovery=50):
|
|
1364
1364
|
|