spacr 0.3.72__tar.gz → 0.3.80__tar.gz

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 (308) hide show
  1. {spacr-0.3.72/spacr.egg-info → spacr-0.3.80}/PKG-INFO +1 -1
  2. spacr-0.3.72/notebooks/old/machine_learning_spacr_nb.ipynb → spacr-0.3.80/notebooks/old/.ipynb_checkpoints/machine_learning_spacr_nb-checkpoint.ipynb +3 -3
  3. spacr-0.3.80/notebooks/old/machine_learning_spacr_nb.ipynb +535 -0
  4. {spacr-0.3.72 → spacr-0.3.80}/setup.py +1 -1
  5. {spacr-0.3.72 → spacr-0.3.80}/spacr/gui_core.py +138 -37
  6. {spacr-0.3.72 → spacr-0.3.80}/spacr/gui_elements.py +1 -1
  7. {spacr-0.3.72 → spacr-0.3.80}/spacr/ml.py +151 -56
  8. {spacr-0.3.72 → spacr-0.3.80}/spacr/settings.py +13 -1
  9. {spacr-0.3.72 → spacr-0.3.80}/spacr/utils.py +8 -1
  10. {spacr-0.3.72 → spacr-0.3.80/spacr.egg-info}/PKG-INFO +1 -1
  11. {spacr-0.3.72 → spacr-0.3.80}/spacr.egg-info/SOURCES.txt +1 -0
  12. {spacr-0.3.72 → spacr-0.3.80}/.readthedocs.yaml +0 -0
  13. {spacr-0.3.72 → spacr-0.3.80}/LICENSE +0 -0
  14. {spacr-0.3.72 → spacr-0.3.80}/MANIFEST.in +0 -0
  15. {spacr-0.3.72 → spacr-0.3.80}/README.rst +0 -0
  16. {spacr-0.3.72 → spacr-0.3.80}/deploy_docs.sh +0 -0
  17. {spacr-0.3.72 → spacr-0.3.80}/docs/requirements.txt +0 -0
  18. {spacr-0.3.72 → spacr-0.3.80}/docs/source/Makefile +0 -0
  19. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/doctrees/environment.pickle +0 -0
  20. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/index.html +0 -0
  21. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_annotate.html +0 -0
  22. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_classify.html +0 -0
  23. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_make_masks.html +0 -0
  24. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_mask.html +0 -0
  25. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_measure.html +0 -0
  26. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_sequencing.html +0 -0
  27. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/app_umap.html +0 -0
  28. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/core.html +0 -0
  29. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/deep_spacr.html +0 -0
  30. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/graph_learning.html +0 -0
  31. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/gui.html +0 -0
  32. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/gui_core.html +0 -0
  33. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/gui_elements.html +0 -0
  34. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/gui_utils.html +0 -0
  35. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/io.html +0 -0
  36. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/logger.html +0 -0
  37. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/measure.html +0 -0
  38. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/plot.html +0 -0
  39. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/sequencing.html +0 -0
  40. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/settings.html +0 -0
  41. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/sim.html +0 -0
  42. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/timelapse.html +0 -0
  43. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_modules/spacr/utils.html +0 -0
  44. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_sources/index.rst.txt +0 -0
  45. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_sources/modules.rst.txt +0 -0
  46. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_sources/spacr.rst.txt +0 -0
  47. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js +0 -0
  48. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/basic.css +0 -0
  49. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/badge_only.css +0 -0
  50. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  51. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  52. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  53. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  54. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
  55. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.svg +0 -0
  56. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  57. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
  58. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  59. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
  60. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  61. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-bold.woff +0 -0
  62. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
  63. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
  64. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  65. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-normal.woff +0 -0
  66. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
  67. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/css/theme.css +0 -0
  68. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/doctools.js +0 -0
  69. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/documentation_options.js +0 -0
  70. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/file.png +0 -0
  71. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/jquery.js +0 -0
  72. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/js/badge_only.js +0 -0
  73. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/js/html5shiv-printshiv.min.js +0 -0
  74. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/js/html5shiv.min.js +0 -0
  75. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/js/theme.js +0 -0
  76. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/language_data.js +0 -0
  77. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/minus.png +0 -0
  78. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/plus.png +0 -0
  79. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/pygments.css +0 -0
  80. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/searchtools.js +0 -0
  81. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/_static/sphinx_highlight.js +0 -0
  82. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/genindex.html +0 -0
  83. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/index.html +0 -0
  84. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/modules.html +0 -0
  85. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/objects.inv +0 -0
  86. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/py-modindex.html +0 -0
  87. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/search.html +0 -0
  88. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/searchindex.js +0 -0
  89. {spacr-0.3.72 → spacr-0.3.80}/docs/source/_build/html/spacr.html +0 -0
  90. {spacr-0.3.72 → spacr-0.3.80}/docs/source/conf.py +0 -0
  91. {spacr-0.3.72 → spacr-0.3.80}/docs/source/index.rst +0 -0
  92. {spacr-0.3.72 → spacr-0.3.80}/docs/source/make.bat +0 -0
  93. {spacr-0.3.72 → spacr-0.3.80}/docs/source/modules.rst +0 -0
  94. {spacr-0.3.72 → spacr-0.3.80}/docs/source/spacr.rst +0 -0
  95. {spacr-0.3.72 → spacr-0.3.80}/environment.yaml +0 -0
  96. {spacr-0.3.72 → spacr-0.3.80}/fonts/OpenSans-Regular.ttf +0 -0
  97. {spacr-0.3.72 → spacr-0.3.80}/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision-checkpoint.ipynb +0 -0
  98. {spacr-0.3.72 → spacr-0.3.80}/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision_sophia-checkpoint.ipynb +0 -0
  99. {spacr-0.3.72 → spacr-0.3.80}/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision_yifan-checkpoint.ipynb +0 -0
  100. {spacr-0.3.72 → spacr-0.3.80}/notebooks/.ipynb_checkpoints/4_spacr_annotate-checkpoint.ipynb +0 -0
  101. {spacr-0.3.72 → spacr-0.3.80}/notebooks/1_spacr_generate_masks.ipynb +0 -0
  102. {spacr-0.3.72 → spacr-0.3.80}/notebooks/2_spacr_generate_mesurments_crop_images.ipynb +0 -0
  103. {spacr-0.3.72 → spacr-0.3.80}/notebooks/3a_spacr_machine_learning.ipynb +0 -0
  104. {spacr-0.3.72 → spacr-0.3.80}/notebooks/3b_spacr_computer_vision.ipynb +0 -0
  105. {spacr-0.3.72 → spacr-0.3.80}/notebooks/3b_spacr_computer_vision_sophia.ipynb +0 -0
  106. {spacr-0.3.72 → spacr-0.3.80}/notebooks/3b_spacr_computer_vision_yifan.ipynb +0 -0
  107. {spacr-0.3.72 → spacr-0.3.80}/notebooks/4_spacr_annotate.ipynb +0 -0
  108. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/Untitled-checkpoint.ipynb +0 -0
  109. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/Untitled1-checkpoint.ipynb +0 -0
  110. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/figure_2-checkpoint.ipynb +0 -0
  111. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/interperate_vision_classes-checkpoint.ipynb +0 -0
  112. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/spacr_image_umap-checkpoint.ipynb +0 -0
  113. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/submodule_1_frequency_analysis-checkpoint.ipynb +0 -0
  114. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/.ipynb_checkpoints/trade_2025-checkpoint.ipynb +0 -0
  115. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/Untitled.ipynb +0 -0
  116. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/Untitled1.ipynb +0 -0
  117. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/cv_scoring_nb.ipynb +0 -0
  118. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/deep_learning_spacr.ipynb +0 -0
  119. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/figure_2.ipynb +0 -0
  120. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/figure_3-Copy1.ipynb +0 -0
  121. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/figure_3.ipynb +0 -0
  122. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/interperate_vision_classes.ipynb +0 -0
  123. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/spacr_0.1_all_settings_git.ipynb +0 -0
  124. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/spacr_0.1_minimal.ipynb +0 -0
  125. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/spacr_image_umap.ipynb +0 -0
  126. {spacr-0.3.72 → spacr-0.3.80}/notebooks/old/trade_2025.ipynb +0 -0
  127. {spacr-0.3.72 → spacr-0.3.80}/notebooks/submodules/submodule_1_frequency_analysis.ipynb +0 -0
  128. {spacr-0.3.72 → spacr-0.3.80}/path/home/carruthers/datasets/plate1/measurements/measurements.db +0 -0
  129. {spacr-0.3.72 → spacr-0.3.80}/path/home/carruthers/datasets/plate1/settings/measure_crop_settings.csv +0 -0
  130. {spacr-0.3.72 → spacr-0.3.80}/path/settings/preprocess_generate_masks_settings.csv +0 -0
  131. {spacr-0.3.72 → spacr-0.3.80}/requirements.txt +0 -0
  132. {spacr-0.3.72 → spacr-0.3.80}/settings/measure_crop_settings.csv +0 -0
  133. {spacr-0.3.72 → spacr-0.3.80}/setup.cfg +0 -0
  134. {spacr-0.3.72 → spacr-0.3.80}/setup_docs.sh +0 -0
  135. {spacr-0.3.72 → spacr-0.3.80}/source/conf.py +0 -0
  136. {spacr-0.3.72 → spacr-0.3.80}/source/index.rst +0 -0
  137. {spacr-0.3.72 → spacr-0.3.80}/source/modules.rst +0 -0
  138. {spacr-0.3.72 → spacr-0.3.80}/source/setup.rst +0 -0
  139. {spacr-0.3.72 → spacr-0.3.80}/source/spacr.rst +0 -0
  140. {spacr-0.3.72 → spacr-0.3.80}/spacr/__init__.py +0 -0
  141. {spacr-0.3.72 → spacr-0.3.80}/spacr/__main__.py +0 -0
  142. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_annotate.py +0 -0
  143. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_classify.py +0 -0
  144. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_make_masks.py +0 -0
  145. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_mask.py +0 -0
  146. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_measure.py +0 -0
  147. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_sequencing.py +0 -0
  148. {spacr-0.3.72 → spacr-0.3.80}/spacr/app_umap.py +0 -0
  149. {spacr-0.3.72 → spacr-0.3.80}/spacr/cellpose.py +0 -0
  150. {spacr-0.3.72 → spacr-0.3.80}/spacr/chat_bot.py +0 -0
  151. {spacr-0.3.72 → spacr-0.3.80}/spacr/core.py +0 -0
  152. {spacr-0.3.72 → spacr-0.3.80}/spacr/deep_spacr.py +0 -0
  153. {spacr-0.3.72 → spacr-0.3.80}/spacr/gui.py +0 -0
  154. {spacr-0.3.72 → spacr-0.3.80}/spacr/gui_utils.py +0 -0
  155. {spacr-0.3.72 → spacr-0.3.80}/spacr/io.py +0 -0
  156. {spacr-0.3.72 → spacr-0.3.80}/spacr/logger.py +0 -0
  157. {spacr-0.3.72 → spacr-0.3.80}/spacr/measure.py +0 -0
  158. {spacr-0.3.72 → spacr-0.3.80}/spacr/mediar.py +0 -0
  159. {spacr-0.3.72 → spacr-0.3.80}/spacr/openai.py +0 -0
  160. {spacr-0.3.72 → spacr-0.3.80}/spacr/plot.py +0 -0
  161. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/.gitignore +0 -0
  162. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/LICENSE +0 -0
  163. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/README.md +0 -0
  164. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/SetupDict.py +0 -0
  165. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/baseline.json +0 -0
  166. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/mediar_example.json +0 -0
  167. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/pred/pred_mediar.json +0 -0
  168. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step1_pretraining/phase1.json +0 -0
  169. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step1_pretraining/phase2.json +0 -0
  170. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step2_finetuning/finetuning1.json +0 -0
  171. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step2_finetuning/finetuning2.json +0 -0
  172. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step3_prediction/base_prediction.json +0 -0
  173. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/config/step3_prediction/ensemble_tta.json +0 -0
  174. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/BasePredictor.py +0 -0
  175. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/BaseTrainer.py +0 -0
  176. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/Baseline/Predictor.py +0 -0
  177. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/Baseline/Trainer.py +0 -0
  178. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/Baseline/__init__.py +0 -0
  179. {spacr-0.3.72 → spacr-0.3.80}/spacr/resources/MEDIAR/core/Baseline/utils.py +0 -0
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{spacr-0.3.72/spacr.egg-info → spacr-0.3.80}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 0.3.72
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+ Version: 0.3.80
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Home-page: https://github.com/EinarOlafsson/spacr
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  Author: Einar Birnir Olafsson
spacr-0.3.72/notebooks/old/machine_learning_spacr_nb.ipynb → spacr-0.3.80/notebooks/old/.ipynb_checkpoints/machine_learning_spacr_nb-checkpoint.ipynb RENAMED
@@ -14,7 +14,7 @@
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  "from spacr.ml import generate_ml_scores\n",
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  "%matplotlib inline\n",
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  "\n",
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- "settings = {'src':'path',\n",
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+ "settings = {'src':'/nas_mnt/carruthers/Einar/tsg101_screen/TSG101SCREEN_20240810_132824/plate1',\n",
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  " 'model_type_ml':'xgboost',\n",
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  " 'heatmap_feature':'predictions',\n",
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  " 'grouping':'mean',\n",
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  " 'minimum_cell_count':25,\n",
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  " 'remove_low_variance_features':True,\n",
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  " 'remove_highly_correlated_features':True,\n",
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- " 'verbose':False,\n",
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- " 'n_jobs':10}\n",
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+ " 'verbose':True,\n",
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+ " 'n_jobs':28}\n",
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  "\n",
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  "results = spacr.ml.generate_ml_scores(settings)"
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  ]