Pinned Repositories
2pRAM-paper
Notebooks accompanying the 2-photon random access mesoscope (2p-RAM) paper
awesome-bioimage-analysis-challenges
A list of awesome bioimage analysis challenges
electron-johnny-five-examples
Example electron apps using johnny-five to control hardware
image-demos
imaging demos
lightning-stream
Render a lighting vizualizations using a stream
napari-training-course
Lectures for a napari training course
psf
Compute microscopy point spread functions (psf)
tactile-coding
Notebooks to accompany sofroniew-vlasov-2015
time-stream
Stream timeseries data to a file
tutorial-scipy2021-bioimage-analysis-fundamentals
Tutorial for SciPy 2021 Bioimage Analysis Fundamentals in Python
sofroniewn's Repositories
sofroniewn/napari-training-course
Lectures for a napari training course
sofroniewn/image-demos
imaging demos
sofroniewn/awesome-bioimage-analysis-challenges
A list of awesome bioimage analysis challenges
sofroniewn/waver
Wave simulations
sofroniewn/proteoscope
Generating images of protein subcellular localization from sequences
sofroniewn/napari
Napari PyQt5 and VisPy based GUI plugin
sofroniewn/rosa
Modeling cell type specific gene expression from the genome
sofroniewn/bio_embeddings
Get protein embeddings from protein sequences
sofroniewn/cytoself
Self-supervised models for encoding protein localization patterns from microscopy images
sofroniewn/DeepRetrosynthesis
sofroniewn/dqc
Differentiable Quantum Chemistry (only Differentiable Density Functional Theory and Hartree Fock at the moment)
sofroniewn/enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
sofroniewn/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
sofroniewn/graphein
Protein Graph Library
sofroniewn/latch_protein_embeddings
Generate protein embeddings via a latch workflow
sofroniewn/latent-diffusion
High-Resolution Image Synthesis with Latent Diffusion Models
sofroniewn/lightning-hydra-template
PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡
sofroniewn/napari-chatgpt
A napari plugin to process and analyse images with chatGPT!
sofroniewn/napari-roi-feedstock
A conda-smithy repository for napari-roi.
sofroniewn/napari-stable-diffusion
A stable diffusion demo for napari
sofroniewn/napari-tomoslice
a napari plugin for visualising electron cryotomograms
sofroniewn/npe2
sofroniewn/paper-qa
LLM Chain for answering questions from documents with citations
sofroniewn/protein_generator
Joint sequence and structure generation with RoseTTAFold sequence space diffusion
sofroniewn/rep-theory-mech-interp
sofroniewn/scBERT
sofroniewn/scFormer
sofroniewn/tf-bind-transformer
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
sofroniewn/website-personal
Personal website
sofroniewn/xitorch
Differentiable scientific computing library