spacr 0.9.2__py3-none-any.whl → 0.9.22__py3-none-any.whl

{spacr-0.9.2.dist-info → spacr-0.9.22.dist-info}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) <year> Adam Veldhousen
+Copyright (c) 2025 Adam Veldhousen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{spacr-0.9.2.dist-info → spacr-0.9.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.2
+Version: 0.9.22
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -174,20 +174,31 @@ Example Notebooks
 
 The following example Jupyter notebooks illustrate common workflows using spaCR.
 
-- `1_spacr_generate_masks.ipynb <Notebooks/1_spacr_generate_masks.ipynb>`_  
+- `Generate masks <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/1_spacr_generate_masks.ipynb>`_  
   *Generate cell, nuclei, and pathogen segmentation masks from microscopy images using Cellpose.*
 
-- `2_spacr_generate_mesurments_crop_images.ipynb <Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
+- `Capture single cell images and measurements <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
   *Extract object-level measurements and crop single-cell images for downstream analysis.*
 
-- `3a_spacr_machine_learning.ipynb <Notebooks/3a_spacr_machine_learning.ipynb>`_  
+- `Machine learning based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3a_spacr_machine_learning.ipynb>`_  
   *Train traditional machine learning models (e.g., XGBoost) to classify cell phenotypes based on extracted features.*
 
-- `3b_spacr_computer_vision.ipynb <Notebooks/3b_spacr_computer_vision.ipynb>`_  
+- `Computer vision based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3b_spacr_computer_vision.ipynb>`_  
   *Train and evaluate deep learning models (PyTorch CNNs/Transformers) on cropped object images.*
 
-- `4_spacr_map_barecodes.ipynb <Notebooks/4_spacr_map_barecodes.ipynb>`_  
+- `Map sequencing barcodes <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/4_spacr_map_barecodes.ipynb>`_  
   *Map sequencing reads to row, column, and gRNA barcodes for CRISPR screen genotype-phenotype mapping.*
 
-- `5_spacr_train_cellpose.ipynb <Notebooks/5_spacr_train_cellpose.ipynb>`_  
+- `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
+
+License
+-------
+spaCR is distributed under the terms of the GNU General Public License v3.0.
+See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ file for details.
+
+How to Cite
+-----------
+If you use spaCR in your research, please cite:  
+Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+

{spacr-0.9.2.dist-info → spacr-0.9.22.dist-info}/RECORD

@@ -102,9 +102,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.9.2.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.9.2.dist-info/METADATA,sha256=vfXoB5rq-qP1Yq4Hj4noXrPKrI-Fs1Q09RN_WTRkQLw,9336
-spacr-0.9.2.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-spacr-0.9.2.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.9.2.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.9.2.dist-info/RECORD,,
+spacr-0.9.22.dist-info/LICENSE,sha256=t0Pov6pnK8thLteoF4xZGmdCwe5mhNwl3OXxLYTGD9U,1081
+spacr-0.9.22.dist-info/METADATA,sha256=2S47OKA9NllqFHRCuTKw8AAi4F2T-TCISGUbAe54V7E,10009
+spacr-0.9.22.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+spacr-0.9.22.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.9.22.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.9.22.dist-info/RECORD,,