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    37 repositories

    • flyvis

      Public
      A connectome-constrained deep mechanistic network (DMN) model of the fruit fly visual system in PyTorch.
      Python
      •
      MIT License
      •27•115•0•1•Updated Mar 26, 2026Mar 26, 2026

    • flybody

      Public
      MuJoCo fruit fly body model and locomotion RL tasks
      reinforcement-learningdeep-learningdrosophila
      reinforcement-learningdeep-learningdrosophilamujoco
      Python
      •
      Apache License 2.0
      •62•512•7•0•Updated Feb 7, 2026Feb 7, 2026

    • optimistix

      Public
      Nonlinear optimisation (root-finding, least squares, ...) in JAX+Equinox. https://docs.kidger.site/optimistix/
      Python
      •
      Apache License 2.0
      •48•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • jhu-janelia-ml-demo

      Public
      Demo notebooks for JHU bootcamp at Janelia
      Jupyter Notebook
      •0•1•0•0•Updated Aug 27, 2025Aug 27, 2025

    • flysim_tutorials

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Jul 22, 2025Jul 22, 2025

    • fouriernet

      Public
      Implementation of Fourier convolution and FourierNet/FourierUNet in JAX and PyTorch
      Jupyter Notebook
      •1•2•0•0•Updated May 27, 2025May 27, 2025

    • snapshotscope

      Public
      Differentiable 4f microscope/phase mask simulation
      Python
      •
      MIT License
      •2•10•0•0•Updated Feb 23, 2025Feb 23, 2025

    • FlySuite

      Public
      This repository contains the environments and models of the flybody.
      Python
      •
      Mozilla Public License 2.0
      •1•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • connectome_reordering

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • flywire_reordering

      Public
      0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • malis

      Public
      MALIS structured loss function for supervised learning of segmentation and clustering
      Python
      •
      MIT License
      •15•18•4•1•Updated Jun 24, 2023Jun 24, 2023

    • gunpowder

      Public
      Data loading DAG for Greentea.
      Python
      •58•0•0•0•Updated Jun 22, 2023Jun 22, 2023

    • DECODE

      Public
      This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
      deep-learninggpupytorch
      deep-learninggpupytorchmicroscopysmlmlocalization-microscopyhigh-density
      Python
      •
      GNU General Public License v3.0
      •33•120•37•0•Updated Jun 22, 2023Jun 22, 2023

    • dvision

      Public
      Python client for the DVID database
      Python
      •1•0•0•0•Updated May 9, 2023May 9, 2023

    • SplinePSF

      Public
      Cuda
      •
      GNU General Public License v3.0
      •3•2•1•1•Updated Dec 12, 2022Dec 12, 2022

    • decode_fish

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •2•1•0•0•Updated Jun 24, 2022Jun 24, 2022

    • stcnn

      Public
      spatiotemporal convnet for modeling visual neuron responses
      HTML
      •0•1•0•0•Updated Jun 14, 2022Jun 14, 2022

    • wormvae

      Public
      Connectome-constrained Latent Variable Model of Whole-brain Neural Activity, ICLR 2022
      Jupyter Notebook
      •3•18•0•0•Updated Apr 26, 2022Apr 26, 2022

    • turagalab.github.io

      Public
      0•0•0•0•Updated Apr 16, 2021Apr 16, 2021

    • vae

      Public
      Model-agnostic variational autoencoder tools
      machine-learningvariational-inferencevariational-autoencoder
      machine-learningvariational-inferencevariational-autoencoder
      Python
      •
      MIT License
      •1•3•0•0•Updated Apr 12, 2020Apr 12, 2020

    • DVSC-Model-Builder

      Public
      Python
      •0•0•0•0•Updated Jul 9, 2018Jul 9, 2018

    • MSRI2018_PupilCodedMicroscope

      Public
      MSRI 2018 summer school (Group 7)
      Jupyter Notebook
      •0•2•0•0•Updated Jul 5, 2018Jul 5, 2018

    • slurm_cluster

      Public
      Configuration files, scripts, and howtos for using the slurm cluster.
      Python
      •0•2•0•0•Updated Apr 19, 2018Apr 19, 2018

    • gunpowder_examples

      Public
      Example scripts for gunpowder training and prediction.
      Python
      •0•0•0•0•Updated Aug 28, 2017Aug 28, 2017

    • system_setup

      Public
      Scripts and docs describing system configuration.
      Makefile
      •0•0•0•0•Updated Aug 4, 2017Aug 4, 2017

    • syntist_progress_report

      Public
      Show progress and current results in syntist project
      Jupyter Notebook
      •0•0•0•0•Updated Jul 18, 2017Jul 18, 2017

    • flyem-dockerfiles

      Public
      Docker Files for Fly EM Software
      Other
      •4•0•0•0•Updated Jul 12, 2017Jul 12, 2017

    • nyroglancer

      Public
      jupyter notebook extension to visualize numpy arrays with the neuroglancer
      Python
      •
      Apache License 2.0
      •10•2•0•0•Updated Jun 30, 2017Jun 30, 2017

    • ipp-tools

      Public
      Collection of IPyParallel tools and helper scripts
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 29, 2017Jun 29, 2017

    • greentea-docker

      Public
      Shell
      •1•0•0•0•Updated May 10, 2017May 10, 2017
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