Repository Index

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

• medical-imaging
• vtk
• itk
• python

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

Neural networks toolbox focused on medical image analysis

• python
• keras
• convolutional-neural-networks
• brain

Kaapana is an open source toolkit for state of the art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging. The name Kaapana comes from the Hawaiian word kaʻāpana, meaning "distributor" or "part".

• imaging
• ai
• cloud-computing
• medical-imaging

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

Medical LLM agent and MRI segmentation workspace built on PharmaLLM, with LangGraph, vLLM, and BEU-Net.

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

⚡ Open-source software for deep learning-based digital pathology

• deep-learning
• machine-learning
• digital-pathology
• computational-pathology

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

• neuroimaging
• reproducibility
• pipeline
• meta-analysis

Axon/Myelin segmentation using Deep Learning

• deep-learning
• machine-learning
• myelin
• axon

Classification and Gradient-based Localization of Chest Radiographs using PyTorch.

• fine-tuning
• vgg16
• resnet18
• densenet121

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

• qa
• mri
• neuroimaging
• niqc

legacy signal processing leveraging afni, ants, fsl, nipy, robex, and wavelet toolbox - brnfswdktm

• fmri-preprocessing
• fmri

a collection of small utlities useful for neuroimaging research

• utilities