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    41 repositories

    • 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•12•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-networksegmentationresnettomographyconnectomicsxrayimage-enhancementunet-3dunet-pytorch
      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-learningsegmentationgansmutex-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
      •296•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
      •30•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