hubmap

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

HuBMAP Data Portal front end

Weighted Masks Fusion (WMF) - Ensembling for Instance Segmentation.

HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.

Utils for loading HuBMAP data formats

Binary segmentation of multi organ tissue units while implementing latest vision transformer architectures

Glomerular Segmentation in Kidney Tissue Images using U-Net.

R client to discover and retrieve data on HuBMAP Data Portal

LinkML schema for ASCB-T tables

HuBMAP & SPARC Linkages

kaggle hubmap kidney segmentation code

Semantic Segmentation to identify glomeruli in kidney images

CFDE Lung Transcriptomics Course

Identify the locations of each functional tissue unit (FTU) in biopsy slides from several different organs.

State-of-the-Art Medical Computer Vision Engine for Multi-Organ Tissue Unit Segmentation (HuBMAP + HPA). Features Organ-Prompted Swin-TransUNet (0.6782 Dice), Macenko Stain Normalization, Monte Carlo Uncertainty Heatmaps, & Streamlit Serving.

Prioritizing Candidate Genetic Variants

Python utility for converting images to zarr chunked arrays

🩸 An applied research project on microvascular instance segmentation in human kidney histology: clinical motivation, two model families (Mask R-CNN, YOLOv8x-seg), a reproducible PyTorch Lightning pipeline, and honest results (best public AP@0.6 = 0.3317).