Repositories list

• 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

  •8•11•0•0•Updated Nov 4, 2024Nov 4, 2024

• cb2_project_analysis

  Public
  Analysis source code for CB2 project

  Jupyter Notebook

  •

  MIT License

  •2•4•1•0•Updated Oct 4, 2024Oct 4, 2024

• run_elastix

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

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

• PPC_inhibitoryMotifs

  Public
  Jupyter Notebook

  •0•0•1•0•Updated Jun 24, 2024Jun 24, 2024

• GridTapeStage

  Public
  GridTape TEM imaging stage

  Python

  •2•2•0•0•Updated Jun 6, 2024Jun 6, 2024

• tem-tomo

  Public
  Code for processing and evaluating TEM tomography data

  Jupyter Notebook

  •1•0•0•0•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 Descriptors, and Mutex Watershed. Built with PyTorch, Daisy, and Gunpowder.

  deep-learninggenerative-adversarial-networksegmentation+ 9resnettomographyconnectomicsxrayimage-enhancementunet-3dunet-pytorch+ 2

  Python

  •

  GNU Affero General Public License v3.0

  •1•3•7•1•Updated Mar 5, 2024Mar 5, 2024

• aedes_public

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 28, 2024Jan 28, 2024

• autoseg

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

  deep-learningsegmentationgans+ 1mutex-watershed

  Python

  •

  Apache License 2.0

  •1•3•0•0•Updated Dec 15, 2023Dec 15, 2023

• ztools

  Public
  A toolbox for Zarr creation/manipulation scripts

  Python

  •0•0•0•0•Updated Nov 2, 2023Nov 2, 2023

• itfbarcode

  Public
  Python

  •5•0•1•0•Updated Aug 22, 2023Aug 22, 2023

• 2p_preprocess_ppc

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

  MATLAB

  •1•0•2•0•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

  •1•1•0•0•Updated Jun 12, 2023Jun 12, 2023

• segway.graph

  Public
  Extraction and analysis of connectomic graph

  Python

  •0•0•0•0•Updated Apr 14, 2023Apr 14, 2023

• cb2_project_analysis_files

  Public
  0•0•0•0•Updated Apr 14, 2023Apr 14, 2023

• segway.synapse.area

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 13, 2023Apr 13, 2023

• segway.mdseg

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 4, 2023Apr 4, 2023

• segway.utils

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 3, 2023Apr 3, 2023

• neuroglancer-mdseg

  Public
  0•0•0•0•Updated Mar 21, 2023Mar 21, 2023

• neuroglancer_mdseg

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •295•0•0•1•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

  •0•1•0•0•Updated Mar 5, 2023Mar 5, 2023

• xpress-challenge-files

  Public
  File repo for the XPRESS challenge

  0•0•0•0•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

  •0•0•0•0•Updated Jan 28, 2023Jan 28, 2023

• xpress

  Public
  HTML

  •0•0•0•0•Updated Dec 13, 2022Dec 13, 2022

• waterz

  Public
  Simple watershed and agglomeration library for affinity graphs.

  C++

  •20•0•0•0•Updated Dec 13, 2022Dec 13, 2022

• lsd

  Public
  🌈

  Python

  •29•0•0•0•Updated Dec 13, 2022Dec 13, 2022

• segway

  Public
  Common scripts for segmentation

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 27, 2022Sep 27, 2022

• cb2_data_availability

  Public
  Data availability for the CB2 dataset

  0•0•0•0•Updated Mar 2, 2022Mar 2, 2022

• gt_pickup_annotation

  Public
  Annotate relative position of section to slot from staining/pickup images

  MATLAB

  •4•0•4•0•Updated Feb 20, 2022Feb 20, 2022

• funlib.show.neuroglancer_v2

  Public
  Scripts and helpers for the neuroglancer WebGL viewer.

  Python

  •13•1•0•0•Updated Oct 8, 2020Oct 8, 2020