Repository Index

AI Toolkit for Healthcare Imaging

• healthcare-imaging
• deep-learning
• medical-image-computing
• medical-image-processing

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.

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

Vision-Language Pathology Foundation Model - Nature Medicine

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

U-Net Brain Tumor Segmentation

• tensorflow
• tensorlayer
• unet
• medical-imaging

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

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

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

Neural networks toolbox focused on medical image analysis

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

Image restoration for fluorescence microscopy

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

The repository host gives no description.

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.

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

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

• histology
• pathology
• wsi-images
• histopathology

The implementation code for "DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction"

• generative-adversarial-network
• mri-reconstruction
• computer-vision
• deep-learning

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

Axon/Myelin segmentation using Deep Learning

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