Repository Index

OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages

• nci-itcr
• nci-qin
• quantitative-imaging
• imaging-informatics

Multi-platform, free open source software for visualization and image computing.

• medical-imaging
• vtk
• itk
• python

[Deprecated] Use Cornerstone3D Instead https://cornerstonejs.org/

• javascript
• cornerstone
• dicom
• medical-imaging

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

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

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

Automated 3D cell detection in very large images

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

PyTorch Connectomics: segmentation toolbox for EM connectomics

• computer-vision
• neuroscience
• connectomics
• pytorch

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration

Automated 3D brain registration with support for multiple species and atlases.

• registration
• atlases
• brain
• neuroscience

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

• neuroimaging
• reproducibility
• pipeline
• meta-analysis

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

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

• qa
• mri
• neuroimaging
• niqc