spacr 0.0.2__tar.gz → 0.0.6__tar.gz

spacr-0.0.6/MANIFEST.in

@@ -0,0 +1 @@
+include spacr/models/cp/*

{spacr-0.0.2/spacr.egg-info → spacr-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.2
+Version: 0.0.6
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,6 +9,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
+Requires-Dist: dgl
 Requires-Dist: torch>=2.2.1
 Requires-Dist: torchvision>=0.17.1
 Requires-Dist: torch-geometric>=2.5.1
@@ -19,6 +20,7 @@ Requires-Dist: scikit-image>=0.22.0
 Requires-Dist: scikit-learn>=1.4.1
 Requires-Dist: seaborn>=0.13.2
 Requires-Dist: matplotlib>=3.8.3
+Requires-Dist: shap>=0.45.0
 Requires-Dist: pillow>=10.2.0
 Requires-Dist: imageio>=2.34.0
 Requires-Dist: scipy>=1.12.0
@@ -29,8 +31,13 @@ Requires-Dist: trackpy>=0.6.2
 Requires-Dist: cellpose>=3.0.6
 Requires-Dist: IPython>=8.18.1
 Requires-Dist: opencv-python-headless>=4.9.0.80
-Requires-Dist: umap>=0.1.1
+Requires-Dist: umap-learn>=0.5.6
 Requires-Dist: ttkthemes>=3.2.2
+Requires-Dist: xgboost>=2.0.3
+Requires-Dist: PyWavelets>=1.6.0
+Requires-Dist: torchcam>=0.4.0
+Requires-Dist: ttf_opensans>=2020.10.30
+Requires-Dist: customtkinter>=5.2.2
 Requires-Dist: lxml>=5.1.0
 Provides-Extra: dev
 Requires-Dist: pytest>=3.9; extra == "dev"
@@ -49,7 +56,7 @@ Requires-Dist: opencv-python; extra == "full"
 <tr>
 <td>
   
-Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions for generating cellpose masks -> single object images and measurements -> annotation and classification of single object images. Spacr uses batch normalization to facilitate accurate segmentation of objects with low foreground representation.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). 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 understand 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.
 
 </td>
 <td>
@@ -62,9 +69,9 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 ## Features
 
-- **Generate Masks:** Generate cellpose masks for cells, nuclei and pathogen images.
+- **Generate Masks:** Generate cellpose masks of cell, nuclei and pathogen objects.
 
-- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity quantiles, shannon-entropy, pearsons and manders correlation, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
+- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
 
 - **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
 
@@ -78,11 +85,13 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 - **Simulations:** Simulate spatial phenotype screens.
 
+- **Sequencing:** Map FASTQ reads to barecode and gRNA barecode metadata.
+
 - **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
 ## Installation
 
-spacr requires Tkinter for its graphical user interface features.
+Requires Tkinter for graphical user interface features.
 
 ### Ubuntu
 
@@ -102,29 +111,8 @@ install spacr with pip
 pip install spacr
 ```
 
-To run spacr GUIs after installing spacr:
+Run spacr GUI:
 
-To generate masks:
-```
-gui_mask
-```
-To generate measurements and cropped images:
-```
-gui_measure
-```
-To curate masks for finetuning cellpose models:
-```
-gui_make_masks
-```
-To annotate paths to images in sql database created in gui_measure:
-```
-gui_annotate
-```
-Train torch CNNs/Transformers to classify single object images.
-```
-gui_classify
-```
-Simulate spatial phenotype screens.
 ```
-gui_sim
+gui
 ```

{spacr-0.0.2 → spacr-0.0.6}/README.md

@@ -8,7 +8,7 @@
 <tr>
 <td>
   
-Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions for generating cellpose masks -> single object images and measurements -> annotation and classification of single object images. Spacr uses batch normalization to facilitate accurate segmentation of objects with low foreground representation.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). 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 understand 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.
 
 </td>
 <td>
@@ -21,9 +21,9 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 ## Features
 
-- **Generate Masks:** Generate cellpose masks for cells, nuclei and pathogen images.
+- **Generate Masks:** Generate cellpose masks of cell, nuclei and pathogen objects.
 
-- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity quantiles, shannon-entropy, pearsons and manders correlation, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
+- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
 
 - **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
 
@@ -37,11 +37,13 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 - **Simulations:** Simulate spatial phenotype screens.
 
+- **Sequencing:** Map FASTQ reads to barecode and gRNA barecode metadata.
+
 - **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
 ## Installation
 
-spacr requires Tkinter for its graphical user interface features.
+Requires Tkinter for graphical user interface features.
 
 ### Ubuntu
 
@@ -61,29 +63,8 @@ install spacr with pip
 pip install spacr
 ```
 
-To run spacr GUIs after installing spacr:
+Run spacr GUI:
 
-To generate masks:
-```
-gui_mask
-```
-To generate measurements and cropped images:
-```
-gui_measure
-```
-To curate masks for finetuning cellpose models:
-```
-gui_make_masks
-```
-To annotate paths to images in sql database created in gui_measure:
-```
-gui_annotate
-```
-Train torch CNNs/Transformers to classify single object images.
-```
-gui_classify
-```
-Simulate spatial phenotype screens.
 ```
-gui_sim
+gui
 ```

{spacr-0.0.2 → spacr-0.0.6}/setup.py

@@ -1,10 +1,28 @@
 from setuptools import setup, find_packages
+import subprocess
+
+# Function to determine the CUDA version
+def get_cuda_version():
+    try:
+        output = subprocess.check_output(['nvcc', '--version'], stderr=subprocess.STDOUT).decode('utf-8')
+        if 'release' in output:
+            return output.split('release ')[1].split(',')[0].replace('.', '')
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        return None
+
+cuda_version = get_cuda_version()
+
+if cuda_version:
+    dgl_dependency = f'dgl-cu{cuda_version}'
+else:
+    dgl_dependency = 'dgl'  # Fallback to CPU version if no CUDA is detected
 
 # Ensure you have read the README.md content into a variable, e.g., `long_description`
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
+    dgl_dependency,
     'torch>=2.2.1',
     'torchvision>=0.17.1',
     'torch-geometric>=2.5.1',
@@ -15,6 +33,7 @@ dependencies = [
     'scikit-learn>=1.4.1',
     'seaborn>=0.13.2',
     'matplotlib>=3.8.3',
+    'shap>=0.45.0',
     'pillow>=10.2.0',
     'imageio>=2.34.0',
     'scipy>=1.12.0',
@@ -25,29 +44,38 @@ dependencies = [
     'cellpose>=3.0.6',
     'IPython>=8.18.1',
     'opencv-python-headless>=4.9.0.80',
-    'umap>=0.1.1',
+    'umap-learn>=0.5.6',
     'ttkthemes>=3.2.2',
+    'xgboost>=2.0.3',
+    'PyWavelets>=1.6.0',
+    'torchcam>=0.4.0',
+    'ttf_opensans>=2020.10.30',
+    'customtkinter>=5.2.2',  
     'lxml>=5.1.0'
 ]
 
 setup(
     name="spacr",
-    version="0.0.2",
+    version="0.0.6",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
     long_description=long_description,
     url="https://github.com/EinarOlafsson/spacr",
     packages=find_packages(exclude=["tests.*", "tests"]),
+    include_package_data=True,
+    package_data={'spacr': ['models/cp/*'],},
     install_requires=dependencies,
     entry_points={
         'console_scripts': [
-            'gui_mask=spacr.gui_mask_app:gui_mask',
-            'gui_measure=spacr.gui_measure_app:gui_measure',
-            'gui_make_masks=spacr.mask_app:gui_make_masks',
-            'gui_annotation=spacr.annotate_app:gui_annotation',
-            'gui_classify=spacr.gui_classify_app:gui_classify',
-            'gui_sim=spacr.gui_sim_app:gui_sim',
+            'mask=spacr.gui_mask_app:gui_mask',
+            'measure=spacr.gui_measure_app:gui_measure',
+            'make_masks=spacr.mask_app:gui_make_masks',
+            'annotate=spacr.annotate_app:gui_annotation',
+            'classify=spacr.gui_classify_app:gui_classify',
+            'sim=spacr.gui_sim_app:gui_sim',
+            'gui=spacr.gui:gui_app',
+            'gui2=spacr.gui_2:gui_app',
         ],
     },
     extras_require={

{spacr-0.0.2 → spacr-0.0.6}/spacr/__init__.py

@@ -8,7 +8,7 @@ from . import plot
 from . import measure
 from . import sim
 from . import timelapse
-from . import train
+from . import deep_spacr
 from . import mask_app
 from . import annotate_app
 from . import graph_learning
@@ -26,7 +26,7 @@ __all__ = [
     "measure",
     "sim",
     "timelapse",
-    "train",
+    "deep_spacr",
     "annotate_app",
     "graph_learning",
     "gui_utils",

{spacr-0.0.2 → spacr-0.0.6}/spacr/__main__.py

@@ -9,7 +9,5 @@ from tqdm import tqdm
 #from spacr import utils, io, version, timelapse, plot, core, mask_app, annotate_app
 import logging
 
-
-
 if __name__ == "__main__":
     main()