senoquant 1.0.0b1__py3-none-any.whl

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Files changed (148) hide show
  1. senoquant/__init__.py +6 -0
  2. senoquant/_reader.py +7 -0
  3. senoquant/_widget.py +33 -0
  4. senoquant/napari.yaml +83 -0
  5. senoquant/reader/__init__.py +5 -0
  6. senoquant/reader/core.py +369 -0
  7. senoquant/tabs/__init__.py +15 -0
  8. senoquant/tabs/batch/__init__.py +10 -0
  9. senoquant/tabs/batch/backend.py +641 -0
  10. senoquant/tabs/batch/config.py +270 -0
  11. senoquant/tabs/batch/frontend.py +1283 -0
  12. senoquant/tabs/batch/io.py +326 -0
  13. senoquant/tabs/batch/layers.py +86 -0
  14. senoquant/tabs/quantification/__init__.py +1 -0
  15. senoquant/tabs/quantification/backend.py +228 -0
  16. senoquant/tabs/quantification/features/__init__.py +80 -0
  17. senoquant/tabs/quantification/features/base.py +142 -0
  18. senoquant/tabs/quantification/features/marker/__init__.py +5 -0
  19. senoquant/tabs/quantification/features/marker/config.py +69 -0
  20. senoquant/tabs/quantification/features/marker/dialog.py +437 -0
  21. senoquant/tabs/quantification/features/marker/export.py +879 -0
  22. senoquant/tabs/quantification/features/marker/feature.py +119 -0
  23. senoquant/tabs/quantification/features/marker/morphology.py +285 -0
  24. senoquant/tabs/quantification/features/marker/rows.py +654 -0
  25. senoquant/tabs/quantification/features/marker/thresholding.py +46 -0
  26. senoquant/tabs/quantification/features/roi.py +346 -0
  27. senoquant/tabs/quantification/features/spots/__init__.py +5 -0
  28. senoquant/tabs/quantification/features/spots/config.py +62 -0
  29. senoquant/tabs/quantification/features/spots/dialog.py +477 -0
  30. senoquant/tabs/quantification/features/spots/export.py +1292 -0
  31. senoquant/tabs/quantification/features/spots/feature.py +112 -0
  32. senoquant/tabs/quantification/features/spots/morphology.py +279 -0
  33. senoquant/tabs/quantification/features/spots/rows.py +241 -0
  34. senoquant/tabs/quantification/frontend.py +815 -0
  35. senoquant/tabs/segmentation/__init__.py +1 -0
  36. senoquant/tabs/segmentation/backend.py +131 -0
  37. senoquant/tabs/segmentation/frontend.py +1009 -0
  38. senoquant/tabs/segmentation/models/__init__.py +5 -0
  39. senoquant/tabs/segmentation/models/base.py +146 -0
  40. senoquant/tabs/segmentation/models/cpsam/details.json +65 -0
  41. senoquant/tabs/segmentation/models/cpsam/model.py +150 -0
  42. senoquant/tabs/segmentation/models/default_2d/details.json +69 -0
  43. senoquant/tabs/segmentation/models/default_2d/model.py +664 -0
  44. senoquant/tabs/segmentation/models/default_3d/details.json +69 -0
  45. senoquant/tabs/segmentation/models/default_3d/model.py +682 -0
  46. senoquant/tabs/segmentation/models/hf.py +71 -0
  47. senoquant/tabs/segmentation/models/nuclear_dilation/__init__.py +1 -0
  48. senoquant/tabs/segmentation/models/nuclear_dilation/details.json +26 -0
  49. senoquant/tabs/segmentation/models/nuclear_dilation/model.py +96 -0
  50. senoquant/tabs/segmentation/models/perinuclear_rings/__init__.py +1 -0
  51. senoquant/tabs/segmentation/models/perinuclear_rings/details.json +34 -0
  52. senoquant/tabs/segmentation/models/perinuclear_rings/model.py +132 -0
  53. senoquant/tabs/segmentation/stardist_onnx_utils/__init__.py +2 -0
  54. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/__init__.py +3 -0
  55. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/data/__init__.py +6 -0
  56. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/data/generate.py +470 -0
  57. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/data/prepare.py +273 -0
  58. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/data/rawdata.py +112 -0
  59. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/data/transform.py +384 -0
  60. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/__init__.py +0 -0
  61. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/blocks.py +184 -0
  62. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/losses.py +79 -0
  63. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/nets.py +165 -0
  64. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/predict.py +467 -0
  65. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/probability.py +67 -0
  66. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/internals/train.py +148 -0
  67. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/io/__init__.py +163 -0
  68. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/__init__.py +52 -0
  69. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/base_model.py +329 -0
  70. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/care_isotropic.py +160 -0
  71. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/care_projection.py +178 -0
  72. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/care_standard.py +446 -0
  73. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/care_upsampling.py +54 -0
  74. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/config.py +254 -0
  75. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/models/pretrained.py +119 -0
  76. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/scripts/__init__.py +0 -0
  77. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/scripts/care_predict.py +180 -0
  78. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/__init__.py +5 -0
  79. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/plot_utils.py +159 -0
  80. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/six.py +18 -0
  81. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/tf.py +644 -0
  82. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/utils.py +272 -0
  83. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/version.py +1 -0
  84. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/docs/source/conf.py +368 -0
  85. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/setup.py +68 -0
  86. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/tests/test_datagen.py +169 -0
  87. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/tests/test_models.py +462 -0
  88. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/tests/test_utils.py +166 -0
  89. senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/tools/create_zip_contents.py +34 -0
  90. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/__init__.py +30 -0
  91. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/big.py +624 -0
  92. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/bioimageio_utils.py +494 -0
  93. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/data/__init__.py +39 -0
  94. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/geometry/__init__.py +10 -0
  95. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/geometry/geom2d.py +215 -0
  96. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/geometry/geom3d.py +349 -0
  97. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/matching.py +483 -0
  98. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/models/__init__.py +28 -0
  99. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/models/base.py +1217 -0
  100. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/models/model2d.py +594 -0
  101. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/models/model3d.py +696 -0
  102. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/nms.py +384 -0
  103. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/plot/__init__.py +2 -0
  104. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/plot/plot.py +74 -0
  105. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/plot/render.py +298 -0
  106. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/rays3d.py +373 -0
  107. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/sample_patches.py +65 -0
  108. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/__init__.py +0 -0
  109. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/predict2d.py +90 -0
  110. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/predict3d.py +93 -0
  111. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/utils.py +408 -0
  112. senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/version.py +1 -0
  113. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/__init__.py +45 -0
  114. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/__init__.py +17 -0
  115. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/cli.py +55 -0
  116. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/core.py +285 -0
  117. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/__init__.py +15 -0
  118. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/cli.py +36 -0
  119. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/divisibility.py +193 -0
  120. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/probe.py +100 -0
  121. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/receptive_field.py +182 -0
  122. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/rf_cli.py +48 -0
  123. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/valid_sizes.py +278 -0
  124. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/post/__init__.py +8 -0
  125. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/post/core.py +157 -0
  126. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/pre/__init__.py +17 -0
  127. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/pre/core.py +226 -0
  128. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/predict/__init__.py +5 -0
  129. senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/predict/core.py +401 -0
  130. senoquant/tabs/settings/__init__.py +1 -0
  131. senoquant/tabs/settings/backend.py +29 -0
  132. senoquant/tabs/settings/frontend.py +19 -0
  133. senoquant/tabs/spots/__init__.py +1 -0
  134. senoquant/tabs/spots/backend.py +139 -0
  135. senoquant/tabs/spots/frontend.py +800 -0
  136. senoquant/tabs/spots/models/__init__.py +5 -0
  137. senoquant/tabs/spots/models/base.py +94 -0
  138. senoquant/tabs/spots/models/rmp/details.json +61 -0
  139. senoquant/tabs/spots/models/rmp/model.py +499 -0
  140. senoquant/tabs/spots/models/udwt/details.json +103 -0
  141. senoquant/tabs/spots/models/udwt/model.py +482 -0
  142. senoquant/utils.py +25 -0
  143. senoquant-1.0.0b1.dist-info/METADATA +193 -0
  144. senoquant-1.0.0b1.dist-info/RECORD +148 -0
  145. senoquant-1.0.0b1.dist-info/WHEEL +5 -0
  146. senoquant-1.0.0b1.dist-info/entry_points.txt +2 -0
  147. senoquant-1.0.0b1.dist-info/licenses/LICENSE +28 -0
  148. senoquant-1.0.0b1.dist-info/top_level.txt +1 -0
senoquant/tabs/segmentation/models/default_3d/details.json ADDED
@@ -0,0 +1,69 @@
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+ {
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+ "name": "default_3d",
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+ "description": "Fine-tuned StarDist 3D model for nuclear segmentation.",
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+ "version": "0.1.0",
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+ "order": 2,
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+ "tasks": {
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+ "nuclear": {
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+ "supported": true
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+ },
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+ "cytoplasmic": {
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+ "supported": false
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+ }
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+ },
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+ "settings": [
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+ {
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+ "key": "object_diameter_px",
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+ "label": "Object diameter (px)",
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+ "type": "float",
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+ "decimals": 1,
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+ "min": 1.0,
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+ "max": 500.0,
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+ "default": 30.0
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+ },
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+ {
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+ "key": "prob_thresh",
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+ "label": "Prob threshold",
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+ "type": "float",
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+ "decimals": 3,
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+ "min": 0.0,
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+ "max": 1.0,
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+ "default": 0.4451190689256302
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+ },
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+ {
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+ "key": "nms_thresh",
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+ "label": "NMS threshold",
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+ "type": "float",
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+ "decimals": 3,
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+ "min": 0.0,
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+ "max": 1.0,
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+ "default": 0.3
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+ },
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+ {
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+ "key": "normalize",
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+ "label": "Normalize",
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+ "type": "bool",
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+ "default": true
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+ },
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+ {
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+ "key": "pmin",
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+ "label": "Percentile min",
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+ "type": "float",
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+ "decimals": 1,
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+ "min": 0.0,
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+ "max": 100.0,
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+ "default": 1.0,
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+ "enabled_by": "normalize"
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+ },
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+ {
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+ "key": "pmax",
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+ "label": "Percentile max",
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+ "type": "float",
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+ "decimals": 1,
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+ "min": 0.0,
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+ "max": 100.0,
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+ "default": 99.8,
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+ "enabled_by": "normalize"
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+ }
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+ ]
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+ }