Paper2Code: Automating Code Generation from Scientific Papers in Machine Learning

A Grammar of Graphics for Python

A very fast 2D concave hull algorithm

Pattern Analysis of SpaTial omics datA

Asynchronous http server graphics device for R.

Public landing page and releases for CellTune.

A Jupyter Notebook / Jupyter Lab extension allowing for tiling of cells for a customizable and flexible layout reducing white space.

Background subtraction for COMET platform

astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

Biomni: a general-purpose biomedical AI agent

Feature extraction from GEOJson nuclei and tissue segmentation maps

DSPy: The framework for programming—not prompting—language models

CIDC Metadata Schemas

Interactive visualization of spatial omics data

Python library for reading and writing scientific data format

Microscopy Metadata for the real world!

Sparse Lazy Array Format (SLAF) for Single-Cell Genomics

This repo powers my blog experiment where ChatGPT manages a real-money micro-cap stock portfolio.

Patches and theory for your software synths

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

Python module that makes working with XML feel like you are working with JSON

Python API and Jupyter widget for Vitessce

The official QuPath extension for InstanSeg

Foundation Model for Multiplex Spatial Proteomic Images

R Package for Single-Cell Dataset Processing and Visualization

Cell2Sentence: Teaching Large Language Models the Language of Biology