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Title: GitHub - AtlasAnalyticsLab/AtlasPatch: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing

Open Graph Title: GitHub - AtlasAnalyticsLab/AtlasPatch: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing

X Title: GitHub - AtlasAnalyticsLab/AtlasPatch: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing

Description: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing - AtlasAnalyticsLab/AtlasPatch

Open Graph Description: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing - AtlasAnalyticsLab/AtlasPatch

X Description: AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing - AtlasAnalyticsLab/AtlasPatch

Opengraph URL: https://github.com/AtlasAnalyticsLab/AtlasPatch

X: @github

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Domain: patch-diff.githubusercontent.com

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https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#atlaspatch-an-efficient-and-scalable-tool-for-whole-slide-image-preprocessing-in-computational-pathology
https://pypi.org/project/atlas-patch/
https://pypi.org/project/atlas-patch/
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch/blob/main/LICENSE
Project Pagehttps://atlasanalyticslab.github.io/AtlasPatch/
Paperhttps://arxiv.org/abs/2602.03998
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https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#table-of-contents
Installationhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#installation
Quick Install (Recommended)https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#quick-install-recommended
OpenSlide Prerequisiteshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#openslide-prerequisites
Optional Encoder Dependencieshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#optional-encoder-dependencies
Alternative Installation Methodshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#alternative-installation-methods
Usage Guidehttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#usage-guide
Pipeline Checkpointshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#pipeline-checkpoints
A - Tissue Detectionhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#a-tissue-detection
B - Patch Coordinate Extractionhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#b-patch-coordinate-extraction
C - Patch Embeddinghttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#c-patch-embedding
D - Patch Writinghttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#d-patch-writing
Visualization Sampleshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#visualization-samples
Process Command Argumentshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#process-command-arguments
Requiredhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#required
Optionalhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#optional
Patch Layouthttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#patch-layout
Segmentation & Extraction Performancehttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#segmentation--extraction-performance
Feature Extractionhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#feature-extraction
Filtering & Qualityhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#filtering--quality
Visualizationhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#visualization
Run Controlhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#run-control
Supported Formatshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#supported-formats
Using Extracted Datahttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#using-extracted-data
Patch Coordinateshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#patch-coordinates
Feature Matriceshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#feature-matrices
Available Feature Extractorshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#available-feature-extractors
Core vision backbones on Natural Imageshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#core-vision-backbones-on-natural-images
Medical- and Pathology-Specific Vision Encodershttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#medical--and-pathology-specific-vision-encoders
CLIP-like modelshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#clip-like-models
Natural Imageshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#natural-images
Medical- and Pathology-Specific CLIPhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#medical--and-pathology-specific-clip
Bring Your Own Encoderhttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#bring-your-own-encoder
SLURM job scriptshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#slurm-job-scripts
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Slide Encodershttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#slide-encoders
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#installation
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#quick-install-recommended
OpenSlide Prerequisiteshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#openslide-prerequisites
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#openslide-prerequisites
OpenSlide Documentationhttps://openslide.org/
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#optional-encoder-dependencies
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#alternative-installation-methods
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#usage-guide
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#pipeline-checkpoints
https://raw.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch/main/assets/images/Checkouts.png
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#a-tissue-detection
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#b-patch-coordinate-extraction
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#c-patch-embedding
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#d-patch-writing
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#visualization-samples
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https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#process-command-arguments
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#required
Available Feature Extractorshttps://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#available-feature-extractors
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#optional
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#patch-layout
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#segmentation--extraction-performance
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#feature-extraction
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#filtering--quality
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#visualization
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#run-control
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#supported-formats
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#using-extracted-data
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#patch-coordinates
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#feature-matrices
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#available-feature-extractors
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#core-vision-backbones-on-natural-images
dinov2_smallhttps://huggingface.co/facebook/dinov2-small
DINOv2: Learning Robust Visual Features without Supervisionhttps://arxiv.org/abs/2304.07193
dinov2_basehttps://huggingface.co/facebook/dinov2-base
DINOv2: Learning Robust Visual Features without Supervisionhttps://arxiv.org/abs/2304.07193
dinov2_largehttps://huggingface.co/facebook/dinov2-large
DINOv2: Learning Robust Visual Features without Supervisionhttps://arxiv.org/abs/2304.07193
dinov2_gianthttps://huggingface.co/facebook/dinov2-giant
DINOv2: Learning Robust Visual Features without Supervisionhttps://arxiv.org/abs/2304.07193
dinov3_vits16https://huggingface.co/facebook/dinov3-vits16-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vits16_plushttps://huggingface.co/facebook/dinov3-vits16plus-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vitb16https://huggingface.co/facebook/dinov3-vitb16-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vitl16https://huggingface.co/facebook/dinov3-vitl16-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vitl16_sathttps://huggingface.co/facebook/dinov3-vitl16-pretrain-sat493m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vith16_plushttps://huggingface.co/facebook/dinov3-vith16plus-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vit7b16https://huggingface.co/facebook/dinov3-vit7b16-pretrain-lvd1689m
DINOv3https://arxiv.org/abs/2508.10104
dinov3_vit7b16_sathttps://huggingface.co/facebook/dinov3-vit7b16-pretrain-sat493m
DINOv3https://arxiv.org/abs/2508.10104
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#medical--and-pathology-specific-vision-encoders
uni_v1https://huggingface.co/MahmoodLab/UNI
Towards a General-Purpose Foundation Model for Computational Pathologyhttps://www.nature.com/articles/s41591-024-02857-3
uni_v2https://huggingface.co/MahmoodLab/UNI2-h
Towards a General-Purpose Foundation Model for Computational Pathologyhttps://www.nature.com/articles/s41591-024-02857-3
phikon_v1https://huggingface.co/owkin/phikon
Scaling Self-Supervised Learning for Histopathology with Masked Image Modelinghttps://www.medrxiv.org/content/10.1101/2023.07.21.23292757v1
phikon_v2https://huggingface.co/owkin/phikon-v2
Phikon-v2, A large and public feature extractor for biomarker predictionhttps://arxiv.org/abs/2409.09173
virchow_v1https://huggingface.co/paige-ai/Virchow
Virchow: A Million-Slide Digital Pathology Foundation Modelhttps://arxiv.org/abs/2309.07778
virchow_v2https://huggingface.co/paige-ai/Virchow2
Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathologyhttps://arxiv.org/abs/2408.00738
prov_gigapathhttps://huggingface.co/prov-gigapath/prov-gigapath
A whole-slide foundation model for digital pathology from real-world datahttps://www.nature.com/articles/s41586-024-07441-w
chief-ctranspathhttps://github.com/hms-dbmi/CHIEF?tab=readme-ov-file
CHIEF: Clinical Histopathology Imaging Evaluation Foundation Modelhttps://www.nature.com/articles/s41586-024-07894-z
midnighthttps://huggingface.co/kaiko-ai/midnight
Training state-of-the-art pathology foundation models with orders of magnitude less datahttps://arxiv.org/abs/2504.05186
muskhttps://github.com/lilab-stanford/MUSK
MUSK: A Vision-Language Foundation Model for Precision Oncologyhttps://www.nature.com/articles/s41586-024-08378-w
openmidnighthttps://sophontai.com/blog/openmidnight
How to Train a State-of-the-Art Pathology Foundation Model with $1.6khttps://sophontai.com/blog/openmidnight
pathorchestrahttps://huggingface.co/AI4Pathology/PathOrchestra
PathOrchestra: A Comprehensive Foundation Model for Computational Pathology with Over 100 Diverse Clinical-Grade Taskshttps://arxiv.org/abs/2503.24345
h_optimus_0https://huggingface.co/bioptimus/H-optimus-0
h_optimus_1https://huggingface.co/bioptimus/H-optimus-1
h0_minihttps://huggingface.co/bioptimus/H0-mini
Distilling foundation models for robust and efficient models in digital pathologyhttps://doi.org/10.48550/arXiv.2501.16239
conch_v1https://huggingface.co/MahmoodLab/CONCH
A visual-language foundation model for computational pathologyhttps://www.nature.com/articles/s41591-024-02856-4
conch_v15https://huggingface.co/MahmoodLab/conchv1_5
From TITANhttps://huggingface.co/MahmoodLab/TITAN
A multimodal whole-slide foundation model for pathologyhttps://www.nature.com/articles/s41591-025-03982-3
hibou_bhttps://huggingface.co/histai/hibou-B
Hibou: A Family of Foundational Vision Transformers for Pathologyhttps://arxiv.org/abs/2406.05074
hibou_lhttps://huggingface.co/histai/hibou-L
Hibou: A Family of Foundational Vision Transformers for Pathologyhttps://arxiv.org/abs/2406.05074
lunit_resnet50_bthttps://huggingface.co/1aurent/resnet50.lunit_bt
Benchmarking Self-Supervised Learning on Diverse Pathology Datasetshttps://openaccess.thecvf.com/content/CVPR2023/papers/Kang_Benchmarking_Self-Supervised_Learning_on_Diverse_Pathology_Datasets_CVPR_2023_paper.pdf
lunit_resnet50_swavhttps://huggingface.co/1aurent/resnet50.lunit_swav
Benchmarking Self-Supervised Learning on Diverse Pathology Datasetshttps://openaccess.thecvf.com/content/CVPR2023/papers/Kang_Benchmarking_Self-Supervised_Learning_on_Diverse_Pathology_Datasets_CVPR_2023_paper.pdf
lunit_resnet50_mocov2https://huggingface.co/1aurent/resnet50.lunit_mocov2
Benchmarking Self-Supervised Learning on Diverse Pathology Datasetshttps://openaccess.thecvf.com/content/CVPR2023/papers/Kang_Benchmarking_Self-Supervised_Learning_on_Diverse_Pathology_Datasets_CVPR_2023_paper.pdf
lunit_vit_small_patch16_dinohttps://huggingface.co/1aurent/vit_small_patch16_224.lunit_dino
Benchmarking Self-Supervised Learning on Diverse Pathology Datasetshttps://openaccess.thecvf.com/content/CVPR2023/papers/Kang_Benchmarking_Self-Supervised_Learning_on_Diverse_Pathology_Datasets_CVPR_2023_paper.pdf
lunit_vit_small_patch8_dinohttps://huggingface.co/1aurent/vit_small_patch8_224.lunit_dino
Benchmarking Self-Supervised Learning on Diverse Pathology Datasetshttps://openaccess.thecvf.com/content/CVPR2023/papers/Kang_Benchmarking_Self-Supervised_Learning_on_Diverse_Pathology_Datasets_CVPR_2023_paper.pdf
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#clip-like-models
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Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
Learning Transferable Visual Models From Natural Language Supervisionhttps://arxiv.org/abs/2103.00020
https://patch-diff.githubusercontent.com/AtlasAnalyticsLab/AtlasPatch#medical--and-pathology-specific-clip
pliphttps://github.com/PathologyFoundation/plip
Pathology Language and Image Pre-Training (PLIP)https://www.nature.com/articles/s41591-023-02504-3
medsigliphttps://huggingface.co/google/medsiglip-448
MedGemma Technical Reporthttps://arxiv.org/abs/2507.05201
quilt_b_32https://quilt1m.github.io/
Quilt-1M: One Million Image-Text Pairs for Histopathologyhttps://arxiv.org/pdf/2306.11207
quilt_b_16https://quilt1m.github.io/
Quilt-1M: One Million Image-Text Pairs for Histopathologyhttps://arxiv.org/pdf/2306.11207
quilt_b_16_pmbhttps://quilt1m.github.io/
Quilt-1M: One Million Image-Text Pairs for Histopathologyhttps://arxiv.org/pdf/2306.11207
biomedcliphttps://huggingface.co/microsoft/BiomedCLIP-PubMedBERT_256-vit_base_patch16_224
BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairshttps://aka.ms/biomedclip-paper
omicliphttps://huggingface.co/WangGuangyuLab/Loki
A visual-omics foundation model to bridge histopathology with spatial transcriptomicshttps://www.nature.com/articles/s41592-025-02707-1
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