cellfinder 1.6.0__py3-none-any.whl → 1.8.0__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.
Files changed (25) hide show
  1. cellfinder/cli_migration_warning.py +3 -1
  2. cellfinder/core/classify/classify.py +50 -4
  3. cellfinder/core/classify/tools.py +13 -3
  4. cellfinder/core/detect/detect.py +73 -58
  5. cellfinder/core/detect/filters/plane/plane_filter.py +1 -1
  6. cellfinder/core/detect/filters/setup_filters.py +31 -12
  7. cellfinder/core/detect/filters/volume/ball_filter.py +5 -5
  8. cellfinder/core/detect/filters/volume/structure_splitting.py +2 -0
  9. cellfinder/core/detect/filters/volume/volume_filter.py +1 -1
  10. cellfinder/core/download/download.py +2 -1
  11. cellfinder/core/main.py +130 -16
  12. cellfinder/core/tools/threading.py +4 -3
  13. cellfinder/core/train/train_yaml.py +4 -13
  14. cellfinder/napari/curation.py +18 -2
  15. cellfinder/napari/detect/detect.py +61 -26
  16. cellfinder/napari/detect/detect_containers.py +31 -8
  17. cellfinder/napari/input_container.py +14 -4
  18. cellfinder/napari/train/train.py +3 -7
  19. cellfinder/napari/train/train_containers.py +0 -2
  20. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/METADATA +5 -4
  21. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/RECORD +25 -25
  22. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/WHEEL +1 -1
  23. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/entry_points.txt +0 -0
  24. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info/licenses}/LICENSE +0 -0
  25. {cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/top_level.txt +0 -0
{cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.2
1
+ Metadata-Version: 2.4
2
2
  Name: cellfinder
3
- Version: 1.6.0
3
+ Version: 1.8.0
4
4
  Summary: Automated 3D cell detection in large microscopy images
5
5
  Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
6
6
  License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: numpy
33
33
  Requires-Dist: scikit-image
34
34
  Requires-Dist: scikit-learn
35
35
  Requires-Dist: keras>=3.7.0
36
- Requires-Dist: torch!=2.4,>=2.1.0
36
+ Requires-Dist: torch>=2.4.1
37
37
  Requires-Dist: tifffile
38
38
  Requires-Dist: tqdm
39
39
  Requires-Dist: qt-niu
@@ -53,9 +53,10 @@ Requires-Dist: brainglobe-napari-io; extra == "napari"
53
53
  Requires-Dist: magicgui; extra == "napari"
54
54
  Requires-Dist: napari-ndtiffs; extra == "napari"
55
55
  Requires-Dist: napari-plugin-engine>=0.1.4; extra == "napari"
56
- Requires-Dist: napari[pyqt5]; extra == "napari"
56
+ Requires-Dist: napari[pyqt5]>=0.6.1; extra == "napari"
57
57
  Requires-Dist: pooch>=1; extra == "napari"
58
58
  Requires-Dist: qtpy; extra == "napari"
59
+ Dynamic: license-file
59
60
 
60
61
  [![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
61
62
  [![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)
{cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/RECORD RENAMED
@@ -1,32 +1,32 @@
1
1
  cellfinder/__init__.py,sha256=S5oQ3EORuyQTMYC4uUuzGKZ23J3Ya6q-1DOBib1KfiA,1166
2
- cellfinder/cli_migration_warning.py,sha256=gPtNrtnXvWpl5q0k_EGAQZg0DwcpCmuBTgpg56n5NfA,1578
2
+ cellfinder/cli_migration_warning.py,sha256=u4nKQiPYmpx0HRqm0PI8wBx78rNiiBSQSGciDoXEq78,1623
3
3
  cellfinder/core/__init__.py,sha256=pRFuQsl78HEK0S6gvhJw70QLbjjSBzP-GFO0AtVaGtk,62
4
- cellfinder/core/main.py,sha256=6PdZxqrAYHauT_K6R4H_u8Eyc3kbrNormySDiWSgTRo,3837
4
+ cellfinder/core/main.py,sha256=QaangjXVi5Sq_fCvMs_PGS-qiFZAsTwymnJ7lhggSno,9497
5
5
  cellfinder/core/types.py,sha256=lTqWE4v0SMM0qLAZJdyAzqV1nLgDtobEpglNJcXt160,106
6
6
  cellfinder/core/classify/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
7
7
  cellfinder/core/classify/augment.py,sha256=8dMbM7KhimM6NMgdMC53oHoCfYj1CIB-h3Yk8CZAxPw,6321
8
- cellfinder/core/classify/classify.py,sha256=UkZJa8DUnyaACx8hazHMi-JSSYosuzBWXkbVhgNo78g,3561
8
+ cellfinder/core/classify/classify.py,sha256=cgZ_2aY8sbQbFo8-43RPPaQMSdS-nt4ukWRzDfWcuOU,5750
9
9
  cellfinder/core/classify/cube_generator.py,sha256=jC5aogTVy213PHouViSR9CgKkuOks3yk6csQC5kRoOE,17125
10
10
  cellfinder/core/classify/resnet.py,sha256=vGa85y_NcQnOXwAt5EtatLx5mrO8IoShCcNKtJ5-EFg,10034
11
- cellfinder/core/classify/tools.py,sha256=s5PEKAsZVbVuoferZ_nqMUM0f2bV_8WEKsdKe3SXEuE,2560
11
+ cellfinder/core/classify/tools.py,sha256=gdWE8cBMlT1pqxBKt6j2az7i7FOMR4N0ds4w9YnBvtQ,2924
12
12
  cellfinder/core/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
13
13
  cellfinder/core/config/cellfinder.conf,sha256=5i8axif7ekMutKDiVnZRs-LiJrgVQljg_beltidqtNk,56
14
14
  cellfinder/core/detect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
15
- cellfinder/core/detect/detect.py,sha256=cd6D3XOzP5HEA_Hb3Ik4AVmNzu0im4sQxV46cCY6izU,8056
15
+ cellfinder/core/detect/detect.py,sha256=jtttIndsVsT0Ww_Dz41GgcVan0nlGzeq24Aulf8g6GQ,9919
16
16
  cellfinder/core/detect/filters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
17
- cellfinder/core/detect/filters/setup_filters.py,sha256=gvWhdGVdGrK_Ab-t0kKPnXaf43qLi78ed_-vNPI0nE4,14554
17
+ cellfinder/core/detect/filters/setup_filters.py,sha256=DIOQe2bvfSTRLPLgDJdzmaPQIgLpmS4lNxihHCRnU5Y,15252
18
18
  cellfinder/core/detect/filters/plane/__init__.py,sha256=lybcPbVDnurEQeq2FiLq0zR8p_ztarQOlajhdh1Q2-4,40
19
19
  cellfinder/core/detect/filters/plane/classical_filter.py,sha256=X5k266tbl9EHRVY5dls53B5IZlmP7U0UB9BsZ1ey_pc,13250
20
- cellfinder/core/detect/filters/plane/plane_filter.py,sha256=6FbAjxgt39_RdGDXC_pQ9ndtZtknuHJeTWtbR8cReEA,6102
20
+ cellfinder/core/detect/filters/plane/plane_filter.py,sha256=4ByEQkF73W5oK_YyrdUwW8GxD-XSrCTtLo4SOT8NCdQ,6127
21
21
  cellfinder/core/detect/filters/plane/tile_walker.py,sha256=IiQibvWKnYlgl9h414fRklV7C2xZ0vXNmJ9t89DhYuI,4863
22
22
  cellfinder/core/detect/filters/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
23
- cellfinder/core/detect/filters/volume/ball_filter.py,sha256=aarEBD6z3ejhNMFdKqKEHi9zLPkopqA3HkzV9RGd7BA,14461
23
+ cellfinder/core/detect/filters/volume/ball_filter.py,sha256=DSBaHXtJ8TM71xT4fgzwL9E1MTE1euNv0vZ6Ozcx5cQ,14491
24
24
  cellfinder/core/detect/filters/volume/structure_detection.py,sha256=AIHq-5u5VFpKBBLEsE1Py-MlndbL8T0zXu0Bq2CI16Y,12916
25
- cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=0LGE8cQ6EJIsKqWWmd087Q3At8m-PUDmmPjCZKV1TdY,10138
26
- cellfinder/core/detect/filters/volume/volume_filter.py,sha256=o9_4IsITedhqkhfwRsIhE53_zLNcFjgQzXbMMddH_q4,20544
25
+ cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=AcQTi_Gddj0vxSVz4JhZz_z16mVBOfCHQlkv8y3uPl4,10190
26
+ cellfinder/core/detect/filters/volume/volume_filter.py,sha256=G9uK6rALRTZufrihzz5TVtE1oGpkXNktrFA4nnOIEaM,20573
27
27
  cellfinder/core/download/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
28
28
  cellfinder/core/download/cli.py,sha256=X9L9ZIkWqs58hX8G8q_0AKN4gk8BhydGxI9nLpdHQQE,1764
29
- cellfinder/core/download/download.py,sha256=YQP4NMM9Xt0rECRJEV5z6RCZNi5uCFhohFnDreH0qHA,3277
29
+ cellfinder/core/download/download.py,sha256=bmPwOm48ApylydasJ8ZvuoQgSSlsb8k4_DL1ikNZrIY,3318
30
30
  cellfinder/core/tools/IO.py,sha256=jK1R_6YahQ_MbPlwg1IM-Fp-din-hLBNq71Jxn3q2WQ,1356
31
31
  cellfinder/core/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
32
32
  cellfinder/core/tools/array_operations.py,sha256=LDbqWA_N2YtxeKS877QYdJRL2FCMC1R1ExJtdb6-vEA,3371
@@ -35,27 +35,27 @@ cellfinder/core/tools/image_processing.py,sha256=z27bGjf3Iv3G4Nt1OYzpEnIYQNc4nNo
35
35
  cellfinder/core/tools/prep.py,sha256=YU4VDyjEsOXn3S3gymEfPUzka-WYiHmR4Q4XdRebhDI,2175
36
36
  cellfinder/core/tools/source_files.py,sha256=vvwsIMe1ULKvXg_x22L75iqvCyMjEbUjJsDFQk3GYzY,856
37
37
  cellfinder/core/tools/system.py,sha256=WvEzPr7v-ohLDnzf4n13TMcN5OYIAXOEkaSmrHzdnwc,2438
38
- cellfinder/core/tools/threading.py,sha256=EmDLF22ZvXJnsWg7g6sv4cZgNweC0YrVw2o7QXjrO9s,14094
38
+ cellfinder/core/tools/threading.py,sha256=mc-XVEfLHj3AFWYcK1Qh4TKmVuW4mNaxgLBlQmBVViU,14154
39
39
  cellfinder/core/tools/tiff.py,sha256=NzIz6wq2GzxmcIhawFMwZADe-uQO2rIG46H7xkpGKLs,2899
40
40
  cellfinder/core/tools/tools.py,sha256=opMGC5GBBsId0dmL8V0KQrI4U70w_D_KtGQYpZNeHYQ,9390
41
41
  cellfinder/core/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
42
- cellfinder/core/train/train_yaml.py,sha256=9QXv2wk24G8hYskMnBij7OngEELUWySK2fH4NFbYWw4,13260
42
+ cellfinder/core/train/train_yaml.py,sha256=tG5FXHZj26PqPUaZCVmFgnvACvIh23mCwEDXwoXv2Hc,13104
43
43
  cellfinder/napari/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
44
- cellfinder/napari/curation.py,sha256=-m9w0SwjmCminZ6FPj_CKHzTeaxyFdI8DL_-s2KfA9c,21426
45
- cellfinder/napari/input_container.py,sha256=tkm0dkPt7kSL8Xkvs1fh8M6vKWw57QLIt_wv74HFkGk,2150
44
+ cellfinder/napari/curation.py,sha256=jItls1SmD5GWNzPlSlF-H73AGgmmBk-PwFO7_gZBY40,22207
45
+ cellfinder/napari/input_container.py,sha256=upTkufWF3aOr9sPPK13C2YwqQ6tygULym8oDXrRLXJs,2510
46
46
  cellfinder/napari/napari.yaml,sha256=WMR1CIAmYIVyQngbdbomTRZLvlDbb6LxsXsvTRClQnE,921
47
47
  cellfinder/napari/sample_data.py,sha256=oUST23q09MM8dxHbUCmO0AjtXG6OlR_32LLqP0EU2UA,732
48
48
  cellfinder/napari/utils.py,sha256=AwTs76M9azutHhHj2yuaKErDEQ5F6pFbIIakBfzen6M,3824
49
49
  cellfinder/napari/detect/__init__.py,sha256=BD9Bg9NTAr6yRTq2A_p58U6j4w5wbY0sdXwhPJ3MSMY,34
50
- cellfinder/napari/detect/detect.py,sha256=EC71KN0AEr49hMjvS8yzvGvfRctqKqn_lNERyx9UAPc,13810
51
- cellfinder/napari/detect/detect_containers.py,sha256=j9NTsIyyDNrhlI2dc7hvc7QlxvI1NRHlCe137v7fsPg,5467
50
+ cellfinder/napari/detect/detect.py,sha256=nFpoxXnDuKTa2nHj62ACvYsiIHzVFXJ6qczomAaBr1g,15723
51
+ cellfinder/napari/detect/detect_containers.py,sha256=rxvSiRszyaVFevJAi8bLMoUog51McfiXWvaQkr-fZQA,6429
52
52
  cellfinder/napari/detect/thread_worker.py,sha256=PWM3OE-FpK-dpdhaE_Gi-2lD3u8sL-SJ13mp0pMhTyI,3078
53
53
  cellfinder/napari/train/__init__.py,sha256=xo4CK-DvSecInGEc2ohcTgQYlH3iylFnGvKTCoq2WkI,35
54
- cellfinder/napari/train/train.py,sha256=5TwGiPkgAStjVuxv3LLzV3-gh_d2Ms7DjdShs0XC7aE,5944
55
- cellfinder/napari/train/train_containers.py,sha256=ryx7g_wSdktB6UbdveM7-YfK5py4pFAcO4Ls8Kre1FA,4388
56
- cellfinder-1.6.0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
57
- cellfinder-1.6.0.dist-info/METADATA,sha256=TvB9qXprasFvS2tcWk6iPtECmqnFsC-0XhflNBLaFaI,7142
58
- cellfinder-1.6.0.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
59
- cellfinder-1.6.0.dist-info/entry_points.txt,sha256=n2n3muDgifENJtTRz1JqYStxvuprROCwmKLt-VxvEHk,248
60
- cellfinder-1.6.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
61
- cellfinder-1.6.0.dist-info/RECORD,,
54
+ cellfinder/napari/train/train.py,sha256=tXrB8j_c293mzhWX5iEs4FvIwV1FpZuaX1rsSP4dgDQ,5830
55
+ cellfinder/napari/train/train_containers.py,sha256=ovPl4ZiH6DUr-CGIYu-iju05z3_rtomyYnCWI6fURKc,4296
56
+ cellfinder-1.8.0.dist-info/licenses/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
57
+ cellfinder-1.8.0.dist-info/METADATA,sha256=m_i5i-J0oyEdjkcipTpZIdcpWjjnxfdfIaqNN6CO4zw,7165
58
+ cellfinder-1.8.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
59
+ cellfinder-1.8.0.dist-info/entry_points.txt,sha256=n2n3muDgifENJtTRz1JqYStxvuprROCwmKLt-VxvEHk,248
60
+ cellfinder-1.8.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
61
+ cellfinder-1.8.0.dist-info/RECORD,,
{cellfinder-1.6.0.dist-info → cellfinder-1.8.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (76.0.0)
2
+ Generator: setuptools (80.9.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5