spacr 1.1.1__tar.gz → 1.1.2__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 (515) hide show
  1. {spacr-1.1.1/spacr.egg-info → spacr-1.1.2}/PKG-INFO +28 -17
  2. {spacr-1.1.1 → spacr-1.1.2}/README.rst +27 -16
  3. {spacr-1.1.1 → spacr-1.1.2}/setup.py +1 -1
  4. spacr-1.1.2/spacr/resources/icons/flow_chart_v3.png +0 -0
  5. spacr-1.1.2/spacr/resources/icons/graphical_abstract.png +0 -0
  6. {spacr-1.1.1 → spacr-1.1.2/spacr.egg-info}/PKG-INFO +28 -17
  7. {spacr-1.1.1 → spacr-1.1.2}/spacr.egg-info/SOURCES.txt +1 -0
  8. spacr-1.1.1/spacr/resources/icons/flow_chart_v3.png +0 -0
  9. {spacr-1.1.1 → spacr-1.1.2}/LICENSE +0 -0
  10. {spacr-1.1.1 → spacr-1.1.2}/MANIFEST.in +0 -0
  11. {spacr-1.1.1 → spacr-1.1.2}/deploy_docs.sh +0 -0
  12. {spacr-1.1.1 → spacr-1.1.2}/docs/.doctrees/environment.pickle +0 -0
  13. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/.doctrees/environment.pickle +0 -0
  14. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/index.html +0 -0
  15. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/core.html +0 -0
  16. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/deep_spacr.html +0 -0
  17. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/gui.html +0 -0
  18. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/gui_core.html +0 -0
  19. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/gui_elements.html +0 -0
  20. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/gui_utils.html +0 -0
  21. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/io.html +0 -0
  22. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/measure.html +0 -0
  23. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/ml.html +0 -0
  24. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/plot.html +0 -0
  25. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/sequencing.html +0 -0
  26. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/settings.html +0 -0
  27. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/sp_stats.html +0 -0
  28. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/spacr_cellpose.html +0 -0
  29. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/submodules.html +0 -0
  30. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/toxo.html +0 -0
  31. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_modules/spacr/utils.html +0 -0
  32. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/index.rst.txt +0 -0
  33. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/core/index.rst.txt +0 -0
  34. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/deep_spacr/index.rst.txt +0 -0
  35. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/gui/index.rst.txt +0 -0
  36. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/gui_core/index.rst.txt +0 -0
  37. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/gui_elements/index.rst.txt +0 -0
  38. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/gui_utils/index.rst.txt +0 -0
  39. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/io/index.rst.txt +0 -0
  40. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/measure/index.rst.txt +0 -0
  41. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/ml/index.rst.txt +0 -0
  42. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/plot/index.rst.txt +0 -0
  43. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/sequencing/index.rst.txt +0 -0
  44. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/settings/index.rst.txt +0 -0
  45. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/sp_stats/index.rst.txt +0 -0
  46. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/spacr_cellpose/index.rst.txt +0 -0
  47. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/submodules/index.rst.txt +0 -0
  48. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/toxo/index.rst.txt +0 -0
  49. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/api/spacr/utils/index.rst.txt +0 -0
  50. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_sources/index.rst.txt +0 -0
  51. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js +0 -0
  52. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/basic.css +0 -0
  53. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/badge_only.css +0 -0
  54. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  55. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  56. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  57. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  58. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
  59. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/fontawesome-webfont.svg +0 -0
  60. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  61. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
  62. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  63. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
  64. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  65. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-bold.woff +0 -0
  66. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
  67. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
  68. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  69. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-normal.woff +0 -0
  70. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
  71. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/css/theme.css +0 -0
  72. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/custom.css +0 -0
  73. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/doctools.js +0 -0
  74. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/documentation_options.js +0 -0
  75. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/file.png +0 -0
  76. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bold.eot +0 -0
  77. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bold.ttf +0 -0
  78. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bold.woff +0 -0
  79. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bold.woff2 +0 -0
  80. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bolditalic.eot +0 -0
  81. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bolditalic.ttf +0 -0
  82. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bolditalic.woff +0 -0
  83. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-bolditalic.woff2 +0 -0
  84. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-italic.eot +0 -0
  85. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-italic.ttf +0 -0
  86. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-italic.woff +0 -0
  87. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-italic.woff2 +0 -0
  88. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-regular.eot +0 -0
  89. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-regular.ttf +0 -0
  90. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-regular.woff +0 -0
  91. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/Lato/lato-regular.woff2 +0 -0
  92. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot +0 -0
  93. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf +0 -0
  94. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff +0 -0
  95. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 +0 -0
  96. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot +0 -0
  97. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf +0 -0
  98. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff +0 -0
  99. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 +0 -0
  100. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/graphviz.css +0 -0
  101. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/jquery.js +0 -0
  102. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/js/badge_only.js +0 -0
  103. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/js/theme.js +0 -0
  104. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/js/versions.js +0 -0
  105. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/language_data.js +0 -0
  106. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/logo_spacr.png +0 -0
  107. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/minus.png +0 -0
  108. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/plus.png +0 -0
  109. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/pygments.css +0 -0
  110. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/searchtools.js +0 -0
  111. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/_static/sphinx_highlight.js +0 -0
  112. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/index.html +0 -0
  113. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/core/index.html +0 -0
  114. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/deep_spacr/index.html +0 -0
  115. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/gui/index.html +0 -0
  116. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/gui_core/index.html +0 -0
  117. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/gui_elements/index.html +0 -0
  118. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/gui_utils/index.html +0 -0
  119. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/io/index.html +0 -0
  120. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/measure/index.html +0 -0
  121. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/ml/index.html +0 -0
  122. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/plot/index.html +0 -0
  123. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/sequencing/index.html +0 -0
  124. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/settings/index.html +0 -0
  125. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/sp_stats/index.html +0 -0
  126. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/spacr_cellpose/index.html +0 -0
  127. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/submodules/index.html +0 -0
  128. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/toxo/index.html +0 -0
  129. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/api/spacr/utils/index.html +0 -0
  130. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/genindex.html +0 -0
  131. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/index.html +0 -0
  132. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/objects.inv +0 -0
  133. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/py-modindex.html +0 -0
  134. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/search.html +0 -0
  135. {spacr-1.1.1 → spacr-1.1.2}/docs/_build/html/searchindex.js +0 -0
  136. {spacr-1.1.1 → spacr-1.1.2}/docs/_images/logo_spacr.png +0 -0
  137. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/SetupDict.html +0 -0
  138. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/BasePredictor.html +0 -0
  139. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/BaseTrainer.html +0 -0
  140. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/Baseline/Predictor.html +0 -0
  141. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/Baseline/Trainer.html +0 -0
  142. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/Baseline/utils.html +0 -0
  143. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/MEDIAR/EnsemblePredictor.html +0 -0
  144. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/MEDIAR/Predictor.html +0 -0
  145. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/MEDIAR/Trainer.html +0 -0
  146. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/MEDIAR/utils.html +0 -0
  147. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/core/utils.html +0 -0
  148. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/evaluate.html +0 -0
  149. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/generate_mapping.html +0 -0
  150. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/index.html +0 -0
  151. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/main.html +0 -0
  152. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/predict.html +0 -0
  153. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_annotate.html +0 -0
  154. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_classify.html +0 -0
  155. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_make_masks.html +0 -0
  156. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_mask.html +0 -0
  157. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_measure.html +0 -0
  158. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_sequencing.html +0 -0
  159. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/app_umap.html +0 -0
  160. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/chat_bot.html +0 -0
  161. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/core.html +0 -0
  162. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/deep_spacr.html +0 -0
  163. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/gui.html +0 -0
  164. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/gui_core.html +0 -0
  165. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/gui_elements.html +0 -0
  166. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/gui_utils.html +0 -0
  167. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/io.html +0 -0
  168. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/logger.html +0 -0
  169. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/measure.html +0 -0
  170. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/mediar.html +0 -0
  171. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/ml.html +0 -0
  172. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/plot.html +0 -0
  173. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/sequencing.html +0 -0
  174. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/settings.html +0 -0
  175. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/sim.html +0 -0
  176. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/sp_stats.html +0 -0
  177. {spacr-1.1.1 → spacr-1.1.2}/docs/_modules/spacr/spacr_cellpose.html +0 -0
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 1.1.1
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+ Version: 1.1.2
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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
@@ -105,33 +105,32 @@ Badges
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  .. |logo| image:: https://raw.githubusercontent.com/EinarOlafsson/spacr/main/spacr/resources/icons/logo_spacr.png
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  :height: 100
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- +------------------------------------------------+----------------------------------------------------+
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- | |logo| | **spaCR** |
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- | | Spatial phenotype analysis of CRISPR- |
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- | | Cas9 screens (spaCR). |
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- +------------------------------------------------+----------------------------------------------------+
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+ |logo| **spaCR**
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+ Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR).
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+
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+ ----------------------------------------
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  The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
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  Features
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  --------
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- - **Generate Masks:** Generate cellpose masks of cell, nuclei, and pathogen objects.
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- - **Object Measurements:** Measurements for each object including scikit-image regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
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+ - **Generate Masks:** Generate `Cellpose <https://github.com/MouseLand/cellpose>`_ masks of cell, nuclei, and pathogen objects.
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+ - **Object Measurements:** Measurements for each object including `scikit-image <https://github.com/scikit-image/scikit-image>`_ regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
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  - **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
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- - **Train CNNs or Transformers:** Train Torch models to classify single object images.
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+ - **Train CNNs or Transformers:** Train `PyTorch <https://github.com/pytorch/pytorch>`_ models to classify single object images.
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  - **Manual Annotation (nightly):** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
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- - **Finetune Cellpose Models (nightly):** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
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+ - **Finetune Cellpose Models (nightly):** Adjust pre-existing `Cellpose <https://github.com/MouseLand/cellpose>`_ models to your specific dataset for improved performance.
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  - **Timelapse Data Support (nightly):** Track objects in timelapse image data.
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- - **Simulations (nightly):** Simulate spatial phenotype screens.
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+ - **Simulations:** Simulate spatial phenotype screens with `spaCRPower <https://github.com/maomlab/spaCRPower>`_.
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  - **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
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  - **Misc (nightly):** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
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  .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
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- :alt: SpaCr workflow
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+ :alt: spaCR workflow
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  :align: center
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- **Overview and data organization of spaCR.**
133
+ **Overview and data organization of spaCR**
135
134
 
136
135
  **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
137
136
  **b.** Output folder structure for each module, including locations for raw and processed images, masks, object-level measurements, datasets, and results.
@@ -150,7 +149,11 @@ If using Windows, switch to Linux—it's free, open-source, and better.
150
149
  brew install libomp hdf5 cmake openssl
151
150
 
152
151
  **Linux GUI requirement:**
153
- SpaCr GUI requires Tkinter. **b.** Downstream submodules available for extended analyses at each stage.
152
+ spaCR GUI requires `Tkinter <https://github.com/python/cpython/tree/main/Lib/tkinter>`_.
153
+
154
+ ::
155
+
156
+ sudo apt install python3-tk
154
157
 
155
158
  **Install stable version (main):**
156
159
 
@@ -201,6 +204,14 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
201
204
  - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_
202
205
  *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
203
206
 
207
+ .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/graphical_abstract.png
208
+ :alt: spaCR workflow
209
+ :align: center
210
+
211
+ **Graphical abstract | Workflow for pooled CRISPR–Cas9 spatial phenotype screening**
212
+
213
+ A pooled population of cells with perturbations (G\ :sub:`1`\ …\ :sub:`i`) is distributed into wells (W\ :sub:`1`\ …\ :sub:`j`) and expanded. Cells from each well (W\ :sub:`j`) are transferred for genotyping by PCR with barcoded primers, followed by next-generation sequencing (NGS) to determine gRNA abundances (R\ :sub:`ij`). In parallel, cells are phenotyped by MaxViT-based image classification, generating an average well classification score (C\ :sub:`j`). Multiple linear regression (MLR) uses C\ :sub:`j` as the response variable and R\ :sub:`ij` as the predictor to estimate the effect size (β\ :sub:`i`) of each gRNA.
214
+
204
215
  Interactive Tutorial (under construction)
205
216
  -----------------------------------------
206
217
 
@@ -211,7 +222,7 @@ Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
211
222
  spaCRPower
212
223
  ----------
213
224
 
214
- Power analasys of pooled perterbation spaCR screens.
225
+ Power analysis of pooled perturbation spaCR screens.
215
226
 
216
227
  `spaCRPower <https://github.com/maomlab/spaCRPower>`_
217
228
 
@@ -235,12 +246,12 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
235
246
  How to Cite
236
247
  -----------
237
248
  If you use spaCR in your research, please cite:
238
- Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
249
+ Olafsson EB, et al. spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
239
250
 
240
251
  Papers Using spaCR
241
252
  -------------------
242
253
  Below are selected publications that have used or cited spaCR:
243
254
 
244
- - Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
255
+ - Olafsson EB, et al. *spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
245
256
  - `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity <https://doi.org/10.1016/j.celrep.2025.115694>`_
246
257
  - `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants <https://doi.org/10.1128/msphere.01011-24>`_
@@ -22,33 +22,32 @@ Badges
22
22
  .. |logo| image:: https://raw.githubusercontent.com/EinarOlafsson/spacr/main/spacr/resources/icons/logo_spacr.png
23
23
  :height: 100
24
24
 
25
- +------------------------------------------------+----------------------------------------------------+
26
- | |logo| | **spaCR** |
27
- | | Spatial phenotype analysis of CRISPR- |
28
- | | Cas9 screens (spaCR). |
29
- +------------------------------------------------+----------------------------------------------------+
25
+ |logo| **spaCR**
26
+ Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR).
27
+
28
+ ----------------------------------------
30
29
 
31
30
  The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
32
31
 
33
32
  Features
34
33
  --------
35
34
 
36
- - **Generate Masks:** Generate cellpose masks of cell, nuclei, and pathogen objects.
37
- - **Object Measurements:** Measurements for each object including scikit-image regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
35
+ - **Generate Masks:** Generate `Cellpose <https://github.com/MouseLand/cellpose>`_ masks of cell, nuclei, and pathogen objects.
36
+ - **Object Measurements:** Measurements for each object including `scikit-image <https://github.com/scikit-image/scikit-image>`_ regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
38
37
  - **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
39
- - **Train CNNs or Transformers:** Train Torch models to classify single object images.
38
+ - **Train CNNs or Transformers:** Train `PyTorch <https://github.com/pytorch/pytorch>`_ models to classify single object images.
40
39
  - **Manual Annotation (nightly):** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
41
- - **Finetune Cellpose Models (nightly):** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
40
+ - **Finetune Cellpose Models (nightly):** Adjust pre-existing `Cellpose <https://github.com/MouseLand/cellpose>`_ models to your specific dataset for improved performance.
42
41
  - **Timelapse Data Support (nightly):** Track objects in timelapse image data.
43
- - **Simulations (nightly):** Simulate spatial phenotype screens.
42
+ - **Simulations:** Simulate spatial phenotype screens with `spaCRPower <https://github.com/maomlab/spaCRPower>`_.
44
43
  - **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
45
44
  - **Misc (nightly):** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
46
45
 
47
46
  .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
48
- :alt: SpaCr workflow
47
+ :alt: spaCR workflow
49
48
  :align: center
50
49
 
51
- **Overview and data organization of spaCR.**
50
+ **Overview and data organization of spaCR**
52
51
 
53
52
  **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
54
53
  **b.** Output folder structure for each module, including locations for raw and processed images, masks, object-level measurements, datasets, and results.
@@ -67,7 +66,11 @@ If using Windows, switch to Linux—it's free, open-source, and better.
67
66
  brew install libomp hdf5 cmake openssl
68
67
 
69
68
  **Linux GUI requirement:**
70
- SpaCr GUI requires Tkinter. **b.** Downstream submodules available for extended analyses at each stage.
69
+ spaCR GUI requires `Tkinter <https://github.com/python/cpython/tree/main/Lib/tkinter>`_.
70
+
71
+ ::
72
+
73
+ sudo apt install python3-tk
71
74
 
72
75
  **Install stable version (main):**
73
76
 
@@ -118,6 +121,14 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
118
121
  - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_
119
122
  *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
120
123
 
124
+ .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/graphical_abstract.png
125
+ :alt: spaCR workflow
126
+ :align: center
127
+
128
+ **Graphical abstract | Workflow for pooled CRISPR–Cas9 spatial phenotype screening**
129
+
130
+ A pooled population of cells with perturbations (G\ :sub:`1`\ …\ :sub:`i`) is distributed into wells (W\ :sub:`1`\ …\ :sub:`j`) and expanded. Cells from each well (W\ :sub:`j`) are transferred for genotyping by PCR with barcoded primers, followed by next-generation sequencing (NGS) to determine gRNA abundances (R\ :sub:`ij`). In parallel, cells are phenotyped by MaxViT-based image classification, generating an average well classification score (C\ :sub:`j`). Multiple linear regression (MLR) uses C\ :sub:`j` as the response variable and R\ :sub:`ij` as the predictor to estimate the effect size (β\ :sub:`i`) of each gRNA.
131
+
121
132
  Interactive Tutorial (under construction)
122
133
  -----------------------------------------
123
134
 
@@ -128,7 +139,7 @@ Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
128
139
  spaCRPower
129
140
  ----------
130
141
 
131
- Power analasys of pooled perterbation spaCR screens.
142
+ Power analysis of pooled perturbation spaCR screens.
132
143
 
133
144
  `spaCRPower <https://github.com/maomlab/spaCRPower>`_
134
145
 
@@ -152,12 +163,12 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
152
163
  How to Cite
153
164
  -----------
154
165
  If you use spaCR in your research, please cite:
155
- Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
166
+ Olafsson EB, et al. spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
156
167
 
157
168
  Papers Using spaCR
158
169
  -------------------
159
170
  Below are selected publications that have used or cited spaCR:
160
171
 
161
- - Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
172
+ - Olafsson EB, et al. *spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
162
173
  - `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity <https://doi.org/10.1016/j.celrep.2025.115694>`_
163
174
  - `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants <https://doi.org/10.1128/msphere.01011-24>`_
@@ -72,7 +72,7 @@ dependencies = [
72
72
  'huggingface-hub>=0.24.0,<0.25'
73
73
  ]
74
74
 
75
- VERSION = "1.1.1"
75
+ VERSION = "1.1.2"
76
76
 
77
77
  setup(
78
78
  name="spacr",
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: spacr
3
- Version: 1.1.1
3
+ Version: 1.1.2
4
4
  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
5
5
  Home-page: https://github.com/EinarOlafsson/spacr
6
6
  Author: Einar Birnir Olafsson
@@ -105,33 +105,32 @@ Badges
105
105
  .. |logo| image:: https://raw.githubusercontent.com/EinarOlafsson/spacr/main/spacr/resources/icons/logo_spacr.png
106
106
  :height: 100
107
107
 
108
- +------------------------------------------------+----------------------------------------------------+
109
- | |logo| | **spaCR** |
110
- | | Spatial phenotype analysis of CRISPR- |
111
- | | Cas9 screens (spaCR). |
112
- +------------------------------------------------+----------------------------------------------------+
108
+ |logo| **spaCR**
109
+ Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR).
110
+
111
+ ----------------------------------------
113
112
 
114
113
  The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
115
114
 
116
115
  Features
117
116
  --------
118
117
 
119
- - **Generate Masks:** Generate cellpose masks of cell, nuclei, and pathogen objects.
120
- - **Object Measurements:** Measurements for each object including scikit-image regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
118
+ - **Generate Masks:** Generate `Cellpose <https://github.com/MouseLand/cellpose>`_ masks of cell, nuclei, and pathogen objects.
119
+ - **Object Measurements:** Measurements for each object including `scikit-image <https://github.com/scikit-image/scikit-image>`_ regionprops, intensity percentiles, shannon-entropy, Pearson’s and Manders’ correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
121
120
  - **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
122
- - **Train CNNs or Transformers:** Train Torch models to classify single object images.
121
+ - **Train CNNs or Transformers:** Train `PyTorch <https://github.com/pytorch/pytorch>`_ models to classify single object images.
123
122
  - **Manual Annotation (nightly):** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
124
- - **Finetune Cellpose Models (nightly):** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
123
+ - **Finetune Cellpose Models (nightly):** Adjust pre-existing `Cellpose <https://github.com/MouseLand/cellpose>`_ models to your specific dataset for improved performance.
125
124
  - **Timelapse Data Support (nightly):** Track objects in timelapse image data.
126
- - **Simulations (nightly):** Simulate spatial phenotype screens.
125
+ - **Simulations:** Simulate spatial phenotype screens with `spaCRPower <https://github.com/maomlab/spaCRPower>`_.
127
126
  - **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
128
127
  - **Misc (nightly):** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
129
128
 
130
129
  .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
131
- :alt: SpaCr workflow
130
+ :alt: spaCR workflow
132
131
  :align: center
133
132
 
134
- **Overview and data organization of spaCR.**
133
+ **Overview and data organization of spaCR**
135
134
 
136
135
  **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
137
136
  **b.** Output folder structure for each module, including locations for raw and processed images, masks, object-level measurements, datasets, and results.
@@ -150,7 +149,11 @@ If using Windows, switch to Linux—it's free, open-source, and better.
150
149
  brew install libomp hdf5 cmake openssl
151
150
 
152
151
  **Linux GUI requirement:**
153
- SpaCr GUI requires Tkinter. **b.** Downstream submodules available for extended analyses at each stage.
152
+ spaCR GUI requires `Tkinter <https://github.com/python/cpython/tree/main/Lib/tkinter>`_.
153
+
154
+ ::
155
+
156
+ sudo apt install python3-tk
154
157
 
155
158
  **Install stable version (main):**
156
159
 
@@ -201,6 +204,14 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
201
204
  - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_
202
205
  *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
203
206
 
207
+ .. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/graphical_abstract.png
208
+ :alt: spaCR workflow
209
+ :align: center
210
+
211
+ **Graphical abstract | Workflow for pooled CRISPR–Cas9 spatial phenotype screening**
212
+
213
+ A pooled population of cells with perturbations (G\ :sub:`1`\ …\ :sub:`i`) is distributed into wells (W\ :sub:`1`\ …\ :sub:`j`) and expanded. Cells from each well (W\ :sub:`j`) are transferred for genotyping by PCR with barcoded primers, followed by next-generation sequencing (NGS) to determine gRNA abundances (R\ :sub:`ij`). In parallel, cells are phenotyped by MaxViT-based image classification, generating an average well classification score (C\ :sub:`j`). Multiple linear regression (MLR) uses C\ :sub:`j` as the response variable and R\ :sub:`ij` as the predictor to estimate the effect size (β\ :sub:`i`) of each gRNA.
214
+
204
215
  Interactive Tutorial (under construction)
205
216
  -----------------------------------------
206
217
 
@@ -211,7 +222,7 @@ Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
211
222
  spaCRPower
212
223
  ----------
213
224
 
214
- Power analasys of pooled perterbation spaCR screens.
225
+ Power analysis of pooled perturbation spaCR screens.
215
226
 
216
227
  `spaCRPower <https://github.com/maomlab/spaCRPower>`_
217
228
 
@@ -235,12 +246,12 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
235
246
  How to Cite
236
247
  -----------
237
248
  If you use spaCR in your research, please cite:
238
- Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
249
+ Olafsson EB, et al. spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
239
250
 
240
251
  Papers Using spaCR
241
252
  -------------------
242
253
  Below are selected publications that have used or cited spaCR:
243
254
 
244
- - Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
255
+ - Olafsson EB, et al. *spaCR: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
245
256
  - `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity <https://doi.org/10.1016/j.celrep.2025.115694>`_
246
257
  - `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants <https://doi.org/10.1128/msphere.01011-24>`_
@@ -494,6 +494,7 @@ spacr/resources/icons/convert.png
494
494
  spacr/resources/icons/default.png
495
495
  spacr/resources/icons/download.png
496
496
  spacr/resources/icons/flow_chart_v3.png
497
+ spacr/resources/icons/graphical_abstract.png
497
498
  spacr/resources/icons/logo_spacr.png
498
499
  spacr/resources/icons/logo_spacr_v1.png
499
500
  spacr/resources/icons/make_masks.png
File without changes
File without changes
File without changes