atlas-patch 1.0.0.post2__py3-none-any.whl → 1.0.0.post4__py3-none-any.whl

atlas_patch/__init__.py

@@ -2,5 +2,5 @@
 
 from . import core, services
 
-__version__ = "1.0.0.post2"
+__version__ = "1.0.0.post4"
 __all__ = ["core", "services", "__version__"]

{atlas_patch-1.0.0.post2.dist-info → atlas_patch-1.0.0.post4.dist-info}/METADATA

@@ -1,11 +1,19 @@
 Metadata-Version: 2.4
 Name: atlas-patch
-Version: 1.0.0.post2
+Version: 1.0.0.post4
 Summary: A Python package for processing and handling whole slide images
-Author: Omar Metwally, Ahmed Alagha
-Author-email: Yousef Kotp <yousefkotp@outlook.com>
+Author: Yousef Kotp, Omar Metwally, Ahmed Alagha
 License: CC-BY-NC-SA-4.0
 Keywords: atlas-patch,whole-slide-image,wsi,tissue-segmentation,patch-extraction,computational-pathology
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: Other/Proprietary License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -53,7 +61,7 @@ Dynamic: license-file
 <!-- TODO: Update paper link (XXXX.XXXXX) once published on arXiv -->
 <p align="center">
   <a href="https://atlasanalyticslab.github.io/AtlasPatch/"><b>Project Page</b></a> |
-  <a href="https://arxiv.org/abs/XXXX.XXXXX"><b>Paper</b></a> |
+  <a href="https://arxiv.org/abs/2602.03998"><b>Paper</b></a> |
   <a href="https://huggingface.co/AtlasAnalyticsLab/AtlasPatch"><b>Hugging Face</b></a> |
   <a href="https://github.com/AtlasAnalyticsLab/AtlasPatch"><b>GitHub</b></a>
 </p>
@@ -275,7 +283,7 @@ Quantitative and qualitative analysis of AtlasPatch tissue detection against exi
   <img src="https://raw.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch/main/assets/images/Comparisons.jpg" alt="AtlasPatch method comparison" width="100%">
 </p>
 
-Representative WSI thumbnails are shown from diverse tissue features and artifact conditions, with tissue masks predicted by thresholding methods (TIAToolbox, CLAM) and deep learning methods (pretrained "non-finetuned" SAM2 model, Trident-QC, Trident-Hest and AtlasPatch), highlighting differences in boundary fidelity, artifact suppression and handling of fragmented tissue (more tools are shown in the appendix). Tissue detection performance is also shown on the held-out test set for AtlasPatch and baseline pipelines, highlighting that AtlasPatch matches or exceeds their segmentation quality. The segmentation complexity–performance trade-off, plotting F1-score against segmentation runtime (on a random set of 100 WSIs), shows AtlasPatch achieves high performance with substantially lower wall-clock time than tile-wise detectors and heuristic pipelines, underscoring its suitability for large-scale WSI preprocessing.
+Representative WSI thumbnails are shown from diverse tissue features and artifact conditions, with tissue masks predicted by thresholding methods (TIAToolbox, CLAM) and deep learning methods (pretrained "non-finetuned" SAM2 model, Trident-QC, Trident-Hest and AtlasPatch), highlighting differences in boundary fidelity, artifact suppression and handling of fragmented tissue. Tissue detection performance is also shown on the held-out test set for AtlasPatch and baseline pipelines, highlighting that AtlasPatch matches or exceeds their segmentation quality. The segmentation complexity–performance trade-off, plotting F1-score against segmentation runtime (on a random set of 100 WSIs), shows AtlasPatch achieves high performance with substantially lower wall-clock time than tile-wise detectors and heuristic pipelines, underscoring its suitability for large-scale WSI preprocessing.
 
 ### Process Command Arguments
 
@@ -705,10 +713,9 @@ If you use AtlasPatch in your research, please cite our paper:
 ```bibtex
 @article{atlaspatch2025,
   title   = {AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology},
-  author  = {Alagha, Ahmed and Leclerc, Christopher and Kotp, Yousef and Abdelwahed, Omar and Moras, Calvin and Rentopoulos, Peter and Rostami, Rose and Nguyen, Bich Ngoc and Baig, Jumanah and Khellaf, Abdelhakim and Trinh, Vincent Quoc-Huy and Mizouni, Rabeb and Otrok, Hadi and Bentahar, Jamal and Hosseini, Mahdi S.},
-  journal = {arXiv},
-  year    = {2025},
-  url     = {TODO: coming soon}
+  author  = {Alagha, Ahmed and Leclerc, Christopher and Kotp, Yousef and Metwally, Omar and Moras, Calvin and Rentopoulos, Peter and Rostami, Ghodsiyeh and Nguyen, Bich Ngoc and Baig, Jumanah and Khellaf, Abdelhakim and Trinh, Vincent Quoc-Huy and Mizouni, Rabeb and Otrok, Hadi and Bentahar, Jamal and Hosseini, Mahdi S.},
+  journal = {arXiv preprint arXiv:2602.03998},
+  year    = {2025}
 }
 ```
 

atlas_patch-1.0.0.post4.dist-info/RECORD

@@ -0,0 +1,8 @@
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+atlas_patch/cli.py,sha256=hLCaFTW_X_oW583GCd_X8oqspkkar0w328VDIsMnHJU,21360
+atlas_patch-1.0.0.post4.dist-info/licenses/LICENSE,sha256=nlArp1_Q_TDOpUl7Q4pLwS8H8CvJMqemBB_WoYuPRqA,20848
+atlas_patch-1.0.0.post4.dist-info/METADATA,sha256=uF6IVtQngvYA319_hSSUWx2cLN4lPKQVLn1Gp94-k7w,36087
+atlas_patch-1.0.0.post4.dist-info/WHEEL,sha256=NDfl-OFbkA03HjLkE6CJK2iNqQtrC5rSyiMF5-Zn27Y,106
+atlas_patch-1.0.0.post4.dist-info/entry_points.txt,sha256=ghEvGjmGrNBkU3PszTcIFFq5Mm3ZEV-jVQmj3BtLmu4,52
+atlas_patch-1.0.0.post4.dist-info/top_level.txt,sha256=HJ6TdtW-ndeALJhIei_xPhGtuCZMeRAAx8YLeY78p7s,12
+atlas_patch-1.0.0.post4.dist-info/RECORD,,

atlas_patch-1.0.0.post2.dist-info/RECORD

@@ -1,8 +0,0 @@
-atlas_patch/__init__.py,sha256=hthRhYJFaYeMf0EpOWMtEMOh2jahHhvNriaffBrsrLM,130
-atlas_patch/cli.py,sha256=hLCaFTW_X_oW583GCd_X8oqspkkar0w328VDIsMnHJU,21360
-atlas_patch-1.0.0.post2.dist-info/licenses/LICENSE,sha256=nlArp1_Q_TDOpUl7Q4pLwS8H8CvJMqemBB_WoYuPRqA,20848
-atlas_patch-1.0.0.post2.dist-info/METADATA,sha256=rY0tI8uBNrbVAnLAWfWjZnJEGXqQkJInRKeiPrj1zU8,35699
-atlas_patch-1.0.0.post2.dist-info/WHEEL,sha256=NDfl-OFbkA03HjLkE6CJK2iNqQtrC5rSyiMF5-Zn27Y,106
-atlas_patch-1.0.0.post2.dist-info/entry_points.txt,sha256=ghEvGjmGrNBkU3PszTcIFFq5Mm3ZEV-jVQmj3BtLmu4,52
-atlas_patch-1.0.0.post2.dist-info/top_level.txt,sha256=HJ6TdtW-ndeALJhIei_xPhGtuCZMeRAAx8YLeY78p7s,12
-atlas_patch-1.0.0.post2.dist-info/RECORD,,