Pinned Repositories
breast-cancer-classification
Classification of Breast Histopathology Images using TensorFlow and Keras. Dataset from Kaggle.
Deeplearning-digital-pathology
Full package for applying deep learning to virtual slides.
DL4MicEverywhere
Bringing the ZeroCostDL4Mic experience running everywhere via easy-to-install docker images
FQPath
No-Reference Focus Quality Assessment of Digital Pathology Images [IEEE TMI 2019]
HPLOC
a benchmark dataset for evidence localization and segmentation in histopathology images
images
OpenAL
Official PyTorch Code of our MICCAI2023 paper OpenAL
qupath-extension-sam
QuPath extension for Segment Anything Model (SAM)
WSI_histology
MATLAB functionality for working with whole slide images of histological slide scans
wsinfer
🔥🚀 Blazingly fast pipeline for patch-based classification in whole slide images
Histopathology Research's Repositories
histopathology/qupath-extension-sam
QuPath extension for Segment Anything Model (SAM)
histopathology/wsinfer
🔥🚀 Blazingly fast pipeline for patch-based classification in whole slide images
histopathology/arriba
Fast and accurate gene fusion detection from RNA-Seq data
histopathology/Awesome-Polyp-Segmentation
histopathology/BiomedParse
BiomedParse: A Foundation Model for Joint Segmentation, Detection, and Recognition of Biomedical Objects Across Nine Modalities
histopathology/DigiPathoImageAnalysis
List of academic institutes/companies working on computer-based digital pathology image analysis
histopathology/digitalsreeni-image-annotator
A python based GUI to annotate images and save annotations as COCO style JSON format.
histopathology/dpat_imageanalysisapi_sdk
SDK for Sectra's ImageAnalysis API for Digital Pathology
histopathology/FrOoDo
histopathology/fseg
Unsupervised Semantic Segmentation for Pathology
histopathology/hibou
Hibou: Foundational Models for Pathology
histopathology/HistoQC
HistoQC is an open-source quality control tool for digital pathology slides
histopathology/i2k2024
histopathology/instanseg
histopathology/ISGPP-model
Model Weights for the ISGPP model for the segmentation of Pancreatic Ductal Adenocarcinoma (PDAC) after neoadjuvant therapy
histopathology/multiview-stitcher
A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
histopathology/nuclei.io
nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
histopathology/omnipose
Omnipose: a high-precision solution for morphology-independent cell segmentation
histopathology/opentile
Python library for reading tiles from wsi tiff-files.
histopathology/PatchSorter
A tool for rapidly labeling objects using deep learning feature embedding
histopathology/predictive_biomarker_collagen_dcis
Collagen biomarker predictive of tamoxifen benefit in DCIS
histopathology/qubalab
Lab for quantitative bioimage analysis experiments in Python
histopathology/qupath-extension-cellpose
an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
histopathology/qupath-extension-instanseg
The official QuPath extension for InstanSeg
histopathology/SAM2PATH
SAM2PATH paper code repo
histopathology/samapi
Segment Anything Model API
histopathology/slideio
histopathology/tissue_segmentation
This script takes whole slide images (typically .svs or .ndpi files; either from biospsies or Cytosponge etc) as an input and returns an image file (typically .png file) of the mask of where the tissue is located (black: tissue, white: background).
histopathology/TITAN
Multimodal Whole Slide Foundation Model for Pathology
histopathology/VoltRon
Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration