histology

QuPath - Bioimage analysis & digital pathology

A Python toolkit for pathology image analysis algorithms.

Two-Stage Convolutional Neural Network for Breast Cancer Histology Image Classification. ICIAR 2018 Grand Challenge on BreAst Cancer Histology images (BACH)

AI-based pathology predicts origins for cancers of unknown primary - Nature

The official deployment of the Digital Slide Archive and HistomicsTK.

Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

A pipeline to segment tissue from the background in histological images

Dataset: landmarks for registration of histology images

Pan-Cancer Integrative Histology-Genomic Analysis via Interpretable Multimodal Deep Learning

Software used by the AGH team during the ANHIR challenge.

a toolbox for manipulation of digital pathology slides and annotations

Code used to create the DeepHistReg submission to the ANHIR challenge.

A Girder plugin for pathology image annotations and analysis.

Fast and Scalable Image Search for Histology

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

The repository contains a simple pipeline for training Nuclei Segmentation Datasets of Histopathology Images.

Segmentation of histological images and fibrosis identification with a convolutional neural network

Deep Learning-based Assessment of Endomyocardial Biopsies

Deep learning pipeline for histology image analysis, with both Tensorflow and PyTorch support.

A virtual slide viewer (virtual microscope) for extremely high-resolution histopathology images. Made with Python, Flask and Leaflet.

An application for exporting and analysing tissue array whole slide image files

2D - 3D slice-to-volume registration pipeline

Generate a package-manager-friendly archive of ABI connectivity maps registered in SAMRI standard space.

slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.

A Python library for segmentation and classification of objects in microscopy images

Generate a package-manager-friendly archive of ABI gene expression maps registered in SAMRI standard space.

Tools that allow processing and visualization to be made for cortical laminae in histological images

ImageJ/Fiji macro that crops any given image stack without having to load it into memory first.

Custom software to allow manual counting of neurons labeled by the pesudorabies (PRV) virus. This software was written for the Texas Biomedical Device Center at UT Dallas. Images must be converted from their native format to the Microsoft "DeepZoom" format. This software relies on Node Webkit and OpenSeadragon.