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

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

GENIE BPC pipeline scripts

A NextFlow workflow to prepare Vectra mIF qptiff files for the HTAN DCC

A vision language model for gigapixel whole slide images in histopathology

Snowflake Administration, Transformations, and Analytics

Bio-Formats Directory Scanner

A pipeline to transform images into valuable analysis items

Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

A Python tiff library

GrAIdient is a deep learning framework that aims at challenging the way we train and run models.

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

Manage scientific data

Basic example of using OME-Zarr in a Nextflow pipeline

INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration

Just a little bit of R to make a pretty figure about connected datasets.

Self-supervised models for encoding protein localization patterns from microscopy images

CHAMMI: A benchmark for channel-adaptive models in microscopy imaging

Functionality to knit RMarkdown documents to Synapse wiki pages.

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

Dataset for Natural Focus Blurr Assessment in Digital Pathology

Official PyTorch and MATLAB implementations of our MICCAI 2020 paper "FocusLiteNN: High Efficiency Focus Quality Assessment for Digital Pathology"

Run HistoQC with the OMERO API

A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.