Segment Anything for Microscopy

BioNeMo Framework: For building and adapting AI models in drug discovery at scale

Single Molecule Footprinting Analysis in Python

ML methods for m6A-calling

Tools for fiberseq data written in rust.

🙌 OpenHands: Code Less, Make More

ExTrack MLE for diffusive noisy single-particle tracks

A bioinformatics tool for working with modified bases

Oxford Nanopore's Basecaller

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

A versatile pairwise aligner for genomic and spliced nucleotide sequences

SEMORE is a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descrip…

An optical-dynamic simulator for experiments supporting a state array paper

Code for processing single-molecule footprinting data on synthetic amplicons (from Doughty*, Hinks*, Schaepe*, et al. 2024).

BiofilmQ: a software tool for quantitative image analysis of microbial biofilm communities

A napari plugin to process and analyse images with chatGPT!

Ray is an AI compute engine. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.

Single-shot autofocus on microscopes using deep learning

A library of free open source icons for science illustrations in biology and chemistry

Python control of micro-manager for customized data acquisition

Python bindings for MMCore, Micro-Manager's device control layer

Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging

Image restoration for fluorescence microscopy

Public releases of TARDIS