spacr 0.9.2__tar.gz → 0.9.21__tar.gz

{spacr-0.9.2/spacr.egg-info → spacr-0.9.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.2
+Version: 0.9.21
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -174,20 +174,21 @@ 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.*
+  

{spacr-0.9.2 → spacr-0.9.21}/README.rst

@@ -92,20 +92,21 @@ 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.*
+  

{spacr-0.9.2 → spacr-0.9.21}/setup.py

@@ -71,7 +71,7 @@ dependencies = [
     'huggingface-hub>=0.24.0,<0.25'
 ]
 
-VERSION = "0.9.2"
+VERSION = "0.9.21"
 
 setup(
     name="spacr",

{spacr-0.9.2 → spacr-0.9.21/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.2
+Version: 0.9.21
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -174,20 +174,21 @@ 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.*
+