histology

There are 2 repositories under histology topic.

qupath / qupath
QuPath - Bioimage analysis & digital pathology
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej opencv groovy histology javafx tissue-microarray-analysis computational-pathology
Language:Java 966
DigitalSlideArchive / HistomicsTK
A Python toolkit for pathology image analysis algorithms.
bioimage-informatics computer-vision digital-slide-archive histology machine-learning medical-image-processing python
Language:Python 362
slideflow
jamesdolezal / slideflow
Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
python machine-learning deep-learning pathology histology computational-pathology whole-slide-imaging histopathology
Language:Python 214
ImagingLab / ICIAR2018
Two-Stage Convolutional Neural Network for Breast Cancer Histology Image Classification. ICIAR 2018 Grand Challenge on BreAst Cancer Histology images (BACH)
deep-learning classification medical-imaging histology pytorch breast-cancer image-classification
Language:Python 203
mahmoodlab / TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
histology pathology wsi-images histopathology cancer-imaging-research cancer-research cancer-detection mahmoodlab deep deep-learning bioimage-analysis bioimage-informatics toad unknown-primary cup
Language:Python 165
mahmoodlab / PORPOISE
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
histology wsi-images pan-cancer-analysis genomics mahmoodlab
Language:Jupyter Notebook 163
axondeepseg / axondeepseg
Axon/Myelin segmentation using Deep Learning
deep-learning machine-learning myelin axon neuropoly spinalcord segmentation electron-microscopy microscopy histology convolutional-neural-networks
Language:Python 112
DigitalSlideArchive / digital_slide_archive
The official deployment of the Digital Slide Archive and HistomicsTK.
histomicstk bioimage-informatics histology digital-slide-archive hacktoberfest
Language:Python 98
mahmoodlab / SISH
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
pathology image-retrieval wsi-images histology image-search-engine histopathology mahmoodlab fish deep-learning vqvae bioimage-analysis bioimage-informatics
Language:Python 89
MICA-MNI / micaopen
Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute
neuroimaging connectomics multimodal histology machine-learning multi-scale networks neuroscience gradients
Language:MATLAB 69
PolarBean / DeepSlice
A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
machine-learning deep-learning histology histological-images brain-imaging automation python brainmap brainmaps neuroscience
Language:Python 69
manuel-munoz-aguirre / PyHIST
A pipeline to segment tissue from the background in histological images
histological-images histology segmentation svs image-segmentation computational-pathology histopathology wsi
Language:Python 55
DigitalSlideArchive / HistomicsUI
A Girder plugin for pathology image annotations and analysis.
bioimage-infomatics digital-slide-archive histology python
Language:JavaScript 52
yiqings / RandStainNA
RandStainNA: Simple and efficient augmentations for histology [MICCAI 2022]
data-augmentation histology miccai-2022 stain-normalization stain-augmentation
Language:Python 39
Borda / dataset-histology-landmarks
Dataset: landmarks for registration of histology images
dataset medical-imaging landmarks image-registration histology anhir
Language:Python 31
ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
cell-segmentation single-cell-analysis imaging-mass-cytometry immunofluorescence histological-images gating tissue-analysis tissue-classification histology bioimage-analysis bioimaging bioimage-tools bioimage-informatics mcd imc life-sciences-image ome-tiff image-analysis-workflows
Language:R 31
AIRMEC / im4MEC
Code for the im4MEC model described in the paper 'Interpretable deep learning model to predict the molecular classification of endometrial cancer from haematoxylin and eosin-stained whole-slide images: a combined analysis of the PORTEC randomised trials and clinical cohorts'.
ai attention-mechanism deep-learning deep-neural-networks deeplearning histology pathology pytorch self-supervised-learning
Language:Python 28
mahmoodlab / CRANE
Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine
pathology whole-slide-imaging weakly-supervised-learning histology biopsy-screening endomyocardial
Language:Python 28
nauyan / NucleiSegmentation
The repository contains a simple pipeline for training Nuclei Segmentation Datasets of Histopathology Images.
deep-learning histological-images histology histopathological-biopsy-images histopathology-images keras medical-imaging tensorflow u-net wsis
Language:Python 26
MWod / ANHIR_MW
Software used by the AGH team during the ANHIR challenge.
anhir image-registration histology microscopy
Language:Python 25
MWod / DeepHistReg
Code used to create the DeepHistReg submission to the ANHIR challenge.
anhir image-registration histology microscopy deep-registration deep-learning medical-image-registration
Language:Python 23
biscuit
jamesdolezal / biscuit
Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding
computational-pathology deep-learning histology machine-learning pathology whole-slide-imaging uncertainty-quantification
Language:Python 20
DSLituiev / slideslicer
a toolbox for manipulation of digital pathology slides and annotations
openslide wsi annotations mask pathology histology slideslicer tissue read-slides
Language:Jupyter Notebook 19
yiqings / HEGnnEnhanceCnn
Graph + Image Bimodal Deep Learning for Histology Image Classification
bimodal cnn deep-learning gnn graph-neural-networks histology medical-imaging multi-modal
Language:Python 15
BiologyTools / BioImager
A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.
histology image-acquisition image-stacks imagej imagej-macro imaging micro-manager microscope microscope-control microscope-stage-controller microscopy plugin scripting whole-slide-imaging
Language:C# 9
c-arthurs / QuArray
An application for exporting and analysing tissue array whole slide image files
histology whole-slide-imaging tissue-analysis immunohistochemistry
Language:Python 7
lely475 / ocelot23algo
Approach that won 3rd place in the OCELOT 2023 Challenge. Multi-organ H&E-based deep learning model for cell detection, applicable for tumor cellularity/ purity/ content estimation.
cell-detection histopathology histopathology-image-analysis tumor-purity-estimation tumor-cellularity-estimation histology
Language:Python 6
xhelenfu / CNN_Segmentation_Histology
Segmentation of histological images and fibrosis identification with a convolutional neural network
segmentation convolutional-neural-networks machine-learning deep-learning deep-neural-networks histological-images histology cardiac-segmentation atrial-fibrillation fibrosis python tensorflow
Language:Python 6
jurgenizer / slidedb
A virtual slide viewer (virtual microscope) for extremely high-resolution histopathology images. Made with Python, Flask and Leaflet.
leaflet python flask pathology microscope histology virtual-microscope microscopy histopathology-images histopathology
Language:HTML 5
slideToolKit
swvanderlaan / slideToolKit
slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.
histology cellprofiler openslide
Language:Shell 5
Fouga / SliVo
2D - 3D slice-to-volume registration pipeline
2d 3d registration feature-detection histology slice volume matlab multi-modal computed-tomography mri
Language:MATLAB 4
BiomechDevOps / Histology-Image-Viewer-and-Converter
Histology Image Viewer and Converter
biomedical-imaging conversion converter freeware histology software svs viewer
3
karthik-d / lung-tumor-classification
Deep-learning based classification pipeline for subtyping lung tumors from histology. Study design and codebase to analyze the impact of nucleus segmentation on subtyping.
classification deep-learning histology histology-images histopathology-images image-processing keras keras-tensorflow lung-cancer-classification lung-cancer-detection opencv papers-with-code published-article python research research-paper research-project research-tool segmentaton tensorflow
Language:Python 3
marleysudbury / detect-diagnose-tumours
Final year project. Analysis and diagnosis of histology images of tumours.
histology machine-learning python tensorflow
Language:Python 3
MBPhys / Partial-Aligner
Partial-Aligner is a napari plugin used for manual registration and histology slide repair
histology image-registration image-restoration napari-plugin
Language:Python 3
yiqings / staintrick
Tricks based on stain variations for histology analysis
histology deep-learning medical-imaging stain-augmentation stain-normalization
Language:Python 2