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    • morphet

      Public
      Jupyter Notebook
      0000Updated Nov 1, 2024Nov 1, 2024
    • tsv

      Public
      Library to render terastitched volumes
      Python
      MIT License
      1010Updated Jun 8, 2024Jun 8, 2024
    • pystripe

      Public
      An image processing package for removing streaks from SPIM images
      Jupyter Notebook
      MIT License
      183111Updated May 14, 2024May 14, 2024
    • A simple utility to generate a precomputed data source as TIF files along with a simple HTTP server of those files.
      Python
      MIT License
      1200Updated Mar 25, 2024Mar 25, 2024
    • nuggt

      Public
      NeUroGlancer Ground Truth - annotate cell centers
      Python
      MIT License
      7910Updated Dec 15, 2023Dec 15, 2023
    • phathom

      Public
      Phenotypic analysis of brain tissue at single-cell resolution
      Jupyter Notebook
      MIT License
      1200Updated Dec 5, 2023Dec 5, 2023
    • unslice

      Public
      Jupyter Notebook
      MIT License
      0000Updated May 5, 2023May 5, 2023
    • Python
      BSD 2-Clause "Simplified" License
      1000Updated May 4, 2023May 4, 2023
    • scout

      Public
      Multiscale hyperdimensional phentypic analysis of organoids
      Jupyter Notebook
      MIT License
      3800Updated Feb 10, 2023Feb 10, 2023
    • A React web-app for rotating two volumes into rough alignment
      JavaScript
      MIT License
      00023Updated Jan 4, 2023Jan 4, 2023
    • leica2tif

      Public
      A quick command-line tool to convert Leica files to TIF.
      Python
      MIT License
      1700Updated Jul 5, 2022Jul 5, 2022
    • Stitch images taken on a diagonal using the SPIM microscope
      Python
      MIT License
      1100Updated Jun 15, 2022Jun 15, 2022
    • dandi-io

      Public
      Remote access to dandisets
      Python
      4000Updated Apr 22, 2022Apr 22, 2022
    • A UI for displaying telemetry data from beegfs-mon
      Python
      MIT License
      0000Updated Feb 4, 2022Feb 4, 2022
    • blockfs

      Public
      A 3D block file storage system optimized for multiprocessing
      Python
      MIT License
      3200Updated Feb 4, 2022Feb 4, 2022
    • pacqproc

      Public
      Post-acquisition processing pipelines for light-sheet microscopy
      Python
      0000Updated Jan 24, 2022Jan 24, 2022
    • Jupyter Notebook
      MIT License
      1500Updated Oct 29, 2021Oct 29, 2021
    • eflash

      Public
      Python
      2000Updated Oct 15, 2021Oct 15, 2021
    • Various data processing tools developed by Nick D. as pipeline practice
      Jupyter Notebook
      0000Updated Sep 7, 2021Sep 7, 2021
    • Uses smartctl to check for failed CEPH drives
      Python
      0200Updated Apr 20, 2021Apr 20, 2021
    • Blockfs to deep zoom translator for the chunglab website.
      Python
      MIT License
      0000Updated Jun 11, 2020Jun 11, 2020
    • rotate2d

      Public
      A quick GUI for rotating ZARR files in 2D.
      Python
      0000Updated May 18, 2020May 18, 2020
    • zheight

      Public
      A utility for displaying a 2D contour map of the z-height of a tissue cut
      Python
      MIT License
      1100Updated Feb 25, 2020Feb 25, 2020
    • User interface for crafting scripts for running PyStripe
      Python
      MIT License
      0000Updated Feb 4, 2020Feb 4, 2020
    • gwdt

      Public
      Grey-weighted distance transform
      Python
      MIT License
      1300Updated Jan 30, 2020Jan 30, 2020
    • A shared-memory wrapper backwards compatible with Python < 3.8
      Python
      MIT License
      1100Updated Dec 10, 2019Dec 10, 2019
    • araw2tif

      Public
      A utility for backing up .raw files to .tif
      Python
      MIT License
      0000Updated Jul 18, 2019Jul 18, 2019
    • Repo for software used in the Chung Lab's Shield paper
      Python
      3200Updated May 14, 2019May 14, 2019
    • Binary assets for shield-2018 docker image
      1100Updated Jan 25, 2019Jan 25, 2019
    • psviewer

      Public
      Pre-stitched viewer of light sheet images
      Python
      MIT License
      0000Updated Dec 17, 2018Dec 17, 2018