Biomedical Informatics Research and Data Science @ Dartmouth

deepslide

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.

HistoGAN

Code for "Generative Image Translation for Data Augmentation in Colorectal Histopathology Images" full paper at ML4H Workshop at NeurIPS 2019.

3dMRISegmentation

Code for NeuroImage: Clinical paper "Automatic post-stroke lesion segmentation on MR images using 3D residual convolutional neural network."

medical-image-preprocessing

Functions for pre-processing large images

MORE

Code for "Multi-Ontology Refined Embeddings (MORE): A Hybrid Multi-Ontology and Corpus-based Semantic Representation Model for Biomedical Concepts" in the Journal of Biomedical Informatics.

titan-rtx-benchmark

Slide2Graph

Graph Convolutional Networks for Whole-Slide Analysis in PyTorch

DifficultyTranslation

Code for "Difficulty Translation in Histopathology Images" full paper at Artificial Intelligence in Medicine (AIME) 2020.

cell-heterogeneity-emtscore

HealthTranscriptAnnotator

Annotates concepts in patient-physician office visit transcripts.

SlidePreprocessing

Extract tissues from WSI

GramViT