spacr 0.0.18__tar.gz → 0.0.20__tar.gz

{spacr-0.0.18/spacr.egg-info → spacr-0.0.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.18
+Version: 0.0.20
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,29 +9,29 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: torch
-Requires-Dist: torchvision
-Requires-Dist: torch-geometric
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: statsmodels
-Requires-Dist: scikit-image
-Requires-Dist: scikit-learn
-Requires-Dist: seaborn
-Requires-Dist: matplotlib
-Requires-Dist: pillow
-Requires-Dist: imageio
-Requires-Dist: scipy
-Requires-Dist: ipywidgets
-Requires-Dist: mahotas
-Requires-Dist: btrack
-Requires-Dist: trackpy
-Requires-Dist: cellpose
-Requires-Dist: IPython
-Requires-Dist: opencv-python-headless
-Requires-Dist: umap
-Requires-Dist: ttkthemes
-Requires-Dist: lxml
+Requires-Dist: torch>=2.2.1
+Requires-Dist: torchvision>=0.17.1
+Requires-Dist: torch-geometric>=2.5.1
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: pandas>=2.2.1
+Requires-Dist: statsmodels>=0.14.1
+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: pillow>=10.2.0
+Requires-Dist: imageio>=2.34.0
+Requires-Dist: scipy>=1.12.0
+Requires-Dist: ipywidgets>=8.1.2
+Requires-Dist: mahotas>=1.4.13
+Requires-Dist: btrack>=0.6.5
+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: ttkthemes>=3.2.2
+Requires-Dist: lxml>=5.1.0
 Provides-Extra: dev
 Requires-Dist: pytest>=3.9; extra == "dev"
 Provides-Extra: headless
@@ -68,16 +68,18 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 - **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.
 
-- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing, 
+- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
 
 - **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
 - **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
 
-- **Timelapse Data Support:** Includes support for analyzing timelapse data.
+- **Timelapse Data Support:** Track objects in timelapse image data.
 
 - **Simulations:** Simulate spatial phenotype screens.
 
+- **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
+
 ## Installation
 
 spacr requires Tkinter for its graphical user interface features.

{spacr-0.0.18 → spacr-0.0.20}/README.md

@@ -27,16 +27,18 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 - **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.
 
-- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing, 
+- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
 
 - **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
 - **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
 
-- **Timelapse Data Support:** Includes support for analyzing timelapse data.
+- **Timelapse Data Support:** Track objects in timelapse image data.
 
 - **Simulations:** Simulate spatial phenotype screens.
 
+- **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
+
 ## Installation
 
 spacr requires Tkinter for its graphical user interface features.

{spacr-0.0.18 → spacr-0.0.20}/setup.py

@@ -5,36 +5,34 @@ with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
-    'torch',
-    'torchvision',
-    'torch-geometric',
-    #'torch-sparse',
-    #'torch-scatter',
-    'numpy',
-    'pandas',
-    'statsmodels',
-    'scikit-image',
-    'scikit-learn',
-    'seaborn',
-    'matplotlib',
-    'pillow',
-    'imageio',
-    'scipy',
-    'ipywidgets',
-    'mahotas',
-    'btrack',
-    'trackpy',
-    'cellpose',
-    'IPython',
-    'opencv-python-headless',
-    'umap',
-    'ttkthemes',
-    'lxml'
+    'torch>=2.2.1',
+    'torchvision>=0.17.1',
+    'torch-geometric>=2.5.1',
+    'numpy>=1.26.4',
+    'pandas>=2.2.1',
+    'statsmodels>=0.14.1',
+    'scikit-image>=0.22.0',
+    'scikit-learn>=1.4.1',
+    'seaborn>=0.13.2',
+    'matplotlib>=3.8.3',
+    'pillow>=10.2.0',
+    'imageio>=2.34.0',
+    'scipy>=1.12.0',
+    'ipywidgets>=8.1.2',
+    'mahotas>=1.4.13',
+    'btrack>=0.6.5',
+    'trackpy>=0.6.2',
+    'cellpose>=3.0.6',
+    'IPython>=8.18.1',
+    'opencv-python-headless>=4.9.0.80',
+    'umap>=0.1.1',
+    'ttkthemes>=3.2.2',
+    'lxml>=5.1.0'
 ]
 
 setup(
     name="spacr",
-    version="0.0.18",
+    version="0.0.20",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",