Stars
Models and scripts to bootstrap and refine 3D instance segmentation models from sparse 2D labels
A library to facilitate machine learning on multi-dimensional images.
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
Drag and drop plotting, data selection, and filtering
Insert and import citations, bibliographies, notes, and PDF annotations from Zotero into Obsidian.
Cataclysm - Dark Days Ahead. A turn-based survival game set in a post-apocalyptic world.
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery (Eid et al., Nature Communications, 2024)
Tools for handling FIB-SEM data and annotations
The U-Net Segmentation plugin for Fiji (ImageJ)
StarDist - Object Detection with Star-convex Shapes
Use gpt to summarize abstracts for a pubmed query
Companion repository for Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions paper
A COVID-19 CoV Genetics (CG) browser to inform therapeutics development
Cloud-native genomic dataframes and batch computing
Fast and multi-platform Spotify client with native GUI
Rapid analysis and visualization of coronavirus genome variation
Open source code for AlphaFold 2.
A library of free open source icons for science illustrations in biology and chemistry
Differential expression of RNA-seq data using the Negative Binomial
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Fitness landscape exploration sandbox for biological sequence design.
Identify cell barcodes from single-cell genomics sequencing experiments