Repositories list

• dorsalhorn-ml

  Public
  Deep learning model for predicting sensory neuron cell types in the mouse dorsal horn.

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• faab

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 27, 2026Feb 27, 2026

• BANC-project

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• LC14

  Public
  Analysis on LC14 to DN connectivity

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 23, 2025Dec 23, 2025

• FANC_auto_recon

  Public
  Code for processing and analyzing the automated reconstruction of the Lee lab's Female Adult Nerve Cord EM dataset

  Python

  •

  GNU General Public License v3.0

  •1010 forks•1515 stars•00 issues•00 pull requests•Updated Dec 5, 2025Dec 5, 2025

• aedes_public

  Public
  license

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 4, 2025Sep 4, 2025

• synister_banc

  Public
  Neurotransmitter predictions for BANC

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 29, 2025Jul 29, 2025

• run_elastix

  Public
  A pipeline for running elastix to register two 3D image volumes

  Shell

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 25, 2025Mar 25, 2025

• itfbarcode

  Public
  Python

  •55 forks•11 star•11 issue•00 pull requests•Updated Dec 4, 2024Dec 4, 2024

• cb2_project_analysis

  Public
  Analysis source code for CB2 project

  Jupyter Notebook

  •

  MIT License

  •22 forks•44 stars•11 issue•00 pull requests•Updated Oct 4, 2024Oct 4, 2024

• PPC_inhibitoryMotifs

  Public
  Jupyter Notebook

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jun 24, 2024Jun 24, 2024

• GridTapeStage

  Public
  GridTape TEM imaging stage

  Python

  •33 forks•33 stars•00 issues•00 pull requests•Updated Jun 6, 2024Jun 6, 2024

• tem-tomo

  Public
  Code for processing and evaluating TEM tomography data

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 31, 2024May 31, 2024

• raygun

  Public
  An image enhancement and segmentation pipeline for generating connectomic reconstructions from X-ray holographic nanotomography, using CycleGANs, Local Shape De…

  deep-learningpytorchgenerative-adversarial-network+ 9

  deep-learningpytorchgenerative-adversarial-networksegmentationresnettomographyconnectomicsxrayimage-enhancementunet-3d+ 2

  Python

  •

  GNU Affero General Public License v3.0

  •11 fork•44 stars•77 issues•11 pull request•Updated Mar 5, 2024Mar 5, 2024

• autoseg

  Public
  Automated deep learning segmentation for large-scale biological datasets.

  deep-learningsegmentationgans+ 1

  deep-learningsegmentationgansmutex-watershed

  Python

  •

  Apache License 2.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Dec 15, 2023Dec 15, 2023

• ztools

  Public
  A toolbox for Zarr creation/manipulation scripts

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 2, 2023Nov 2, 2023

• 2p_preprocess_ppc

  Public
  align imaging and behavior data, motion correct, acq2p init

  MATLAB

  •22 forks•00 stars•22 issues•00 pull requests•Updated Jul 24, 2023Jul 24, 2023

• GridTape_VNC_paper

  Public
  Resources related to the GridTape/VNC EM dataset paper

  Python

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jun 12, 2023Jun 12, 2023

• segway.graph

  Public
  Extraction and analysis of connectomic graph

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2023Apr 14, 2023

• cb2_project_analysis_files

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2023Apr 14, 2023

• segway.synapse.area

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2023Apr 13, 2023

• segway.mdseg

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• segway.utils

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2023Apr 3, 2023

• neuroglancer-mdseg

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 21, 2023Mar 21, 2023

• neuroglancer_mdseg

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •359359 forks•00 stars•00 issues•11 pull request•Updated Mar 21, 2023Mar 21, 2023

• pymaid_addons

  Public
  A collection of modules built on top of pymaid, a python package for interacting with CATMAID reconstructions.

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 5, 2023Mar 5, 2023

• xpress-challenge-files

  Public
  File repo for the XPRESS challenge

  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 4, 2023Feb 4, 2023

• cb2-meshes

  Public
  Surface renderings of neurons in the paper "Structured cerebellar connectivity supports resilient pattern separation"

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 28, 2023Jan 28, 2023

• xpress

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• waterz

  Public
  Simple watershed and agglomeration library for affinity graphs.

  C++

  •2828 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022