wuusn

CellProfiler

An open-source application for biological image analysis

prov-gigapath

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

statannot

add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot

consensusclustering

Python implementation of Consensus Clustering by Monti et al. (2003)

UNI

Towards a general-purpose foundation model for computational pathology - Nature Medicine

CONCH

A vision-language foundation model for computational pathology - Nature Medicine

HistoMIL

A Python package for handling histopathology whole-slide images using multiple instance learning (MIL) techniques.

Lifelong-nnUNet

nnUNet-for-pathology

Adapted nnUNet framework with additional features to suit the requirements for pathology applications

pathology-whole-slide-data

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

hd_wsi

SAMPath

Repository for "SAM-Path: A Segment Anything Model for Semantic Segmentation in Digital Pathology" (MedAGI2023, MICCAI2023 workshop)

torch-staintools

Pytorch-adaptation of GPU-accelerated StainTool's stain normalization algorithms

Dino_V2

Dino V2 for Classification, PCA Visualization, Instance Retrival: https://arxiv.org/abs/2304.07193

dinov2

PyTorch code and models for the DINOv2 self-supervised learning method.

SimMIM

This is an official implementation for "SimMIM: A Simple Framework for Masked Image Modeling".

DualQueryMIL

Dual-Query Multiple Instance Learning for Dynamic Meta-Embedding based Tumor Classification

ips

PyTorch Implementation of Iterative Patch Selection for High-Resolution Image Recognition

UIOS

sc_MTOP

sc-MTOP is an analysis framework based on deep learning and computational pathology. This framework aims to characterize the tumor ecosystem diversity at the single-cell level. This code provide 1) Hover-Net-based nuclear segmentation and classification; 2) Nuclear morphological and texture feature extraction; 3) Multi-level pairwise nuclear graph construction and spatial topological feature extraction.

diffusion

Denoising Diffusion Probabilistic Models

SISH

Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

PyTorch-Image-Models-Multi-Label-Classification

Multi-label classification based on timm.

Awesome-Multi-Task-Learning

An up-to-date list of works on Multi-Task Learning

ITAS3D

Image-translation-assisted segmentation in 3D

scPretrain

scPretrain: Multi-task self-supervised learning for cell type classification

gigassl

Repository for the Giga-SSL paper

perceiver-io

A PyTorch implementation of Perceiver, Perceiver IO and Perceiver AR with PyTorch Lightning scripts for distributed training

UniverSeg

UniverSeg: Universal Medical Image Segmentation

perceiver-pytorch

Implementation of Perceiver, General Perception with Iterative Attention, in Pytorch