Repository Index

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning

⚡High Performance DICOM Medical Image Parser in Go.

• dicom
• dicom-images
• golang
• golang-library

3D medical imaging reconstruction software

• dicom
• dicom-viewer
• magnetic-resonance-imaging
• medical-image-processing

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

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

• histology
• wsi-images
• pan-cancer-analysis
• genomics

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

Converts medical images to more displayable formats, e.g. NIfTI to jpg.

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

• histology
• pathology
• wsi-images
• histopathology

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

• minerva
• microscopy
• ome
• immunofluorescence

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance

• qa
• mri
• neuroimaging
• niqc

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images