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    38 repositories

    • morphet

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

    • tsv

      Public
      Library to render terastitched volumes
      Python
      •
      MIT License
      •1•0•1•0•Updated Jun 8, 2024Jun 8, 2024

    • pystripe

      Public
      An image processing package for removing streaks from SPIM images
      Jupyter Notebook
      •
      MIT License
      •18•31•1•1•Updated May 14, 2024May 14, 2024

    • precomputed-tif

      Public
      A simple utility to generate a precomputed data source as TIF files along with a simple HTTP server of those files.
      Python
      •
      MIT License
      •1•2•0•0•Updated Mar 25, 2024Mar 25, 2024

    • nuggt

      Public
      NeUroGlancer Ground Truth - annotate cell centers
      Python
      •
      MIT License
      •7•9•1•0•Updated Dec 15, 2023Dec 15, 2023

    • phathom

      Public
      Phenotypic analysis of brain tissue at single-cell resolution
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Dec 5, 2023Dec 5, 2023

    • unslice

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 5, 2023May 5, 2023

    • axon-centerline-detection

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•0•0•Updated May 4, 2023May 4, 2023

    • scout

      Public
      Multiscale hyperdimensional phentypic analysis of organoids
      Jupyter Notebook
      •
      MIT License
      •3•8•0•0•Updated Feb 10, 2023Feb 10, 2023

    • rigid-rotate

      Public
      A React web-app for rotating two volumes into rough alignment
      JavaScript
      •
      MIT License
      •0•0•0•23•Updated Jan 4, 2023Jan 4, 2023

    • leica2tif

      Public
      A quick command-line tool to convert Leica files to TIF.
      Python
      •
      MIT License
      •1•7•0•0•Updated Jul 5, 2022Jul 5, 2022

    • spimstitch

      Public
      Stitch images taken on a diagonal using the SPIM microscope
      Python
      •
      MIT License
      •1•1•0•0•Updated Jun 15, 2022Jun 15, 2022

    • dandi-io

      Public
      Remote access to dandisets
      Python
      •4•0•0•0•Updated Apr 22, 2022Apr 22, 2022

    • beegfsmonitor

      Public
      A UI for displaying telemetry data from beegfs-mon
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2022Feb 4, 2022

    • blockfs

      Public
      A 3D block file storage system optimized for multiprocessing
      Python
      •
      MIT License
      •3•2•0•0•Updated Feb 4, 2022Feb 4, 2022

    • pacqproc

      Public
      Post-acquisition processing pipelines for light-sheet microscopy
      Python
      •0•0•0•0•Updated Jan 24, 2022Jan 24, 2022

    • bmtrap_2021

      Public
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Oct 29, 2021Oct 29, 2021

    • eflash_2018

      Public
      Python
      •2•0•0•0•Updated Oct 15, 2021Oct 15, 2021

    • data-processing-tools

      Public
      Various data processing tools developed by Nick D. as pipeline practice
      Jupyter Notebook
      •0•0•0•0•Updated Sep 7, 2021Sep 7, 2021

    • ceph-smartctl

      Public
      Uses smartctl to check for failed CEPH drives
      Python
      •0•2•0•0•Updated Apr 20, 2021Apr 20, 2021

    • chunglab_dz

      Public
      Blockfs to deep zoom translator for the chunglab website.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2020Jun 11, 2020

    • rotate2d

      Public
      A quick GUI for rotating ZARR files in 2D.
      Python
      •0•0•0•0•Updated 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
      •1•1•0•0•Updated Feb 25, 2020Feb 25, 2020

    • pystripe-ui

      Public
      User interface for crafting scripts for running PyStripe
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2020Feb 4, 2020

    • gwdt

      Public
      Grey-weighted distance transform
      Python
      •
      MIT License
      •1•3•0•0•Updated Jan 30, 2020Jan 30, 2020

    • mp_shared_memory

      Public
      A shared-memory wrapper backwards compatible with Python < 3.8
      Python
      •
      MIT License
      •1•1•0•0•Updated Dec 10, 2019Dec 10, 2019

    • araw2tif

      Public
      A utility for backing up .raw files to .tif
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 18, 2019Jul 18, 2019

    • shield-2018

      Public
      Repo for software used in the Chung Lab's Shield paper
      Python
      •3•2•0•0•Updated May 14, 2019May 14, 2019

    • shield-2018-assets

      Public
      Binary assets for shield-2018 docker image
      1•1•0•0•Updated Jan 25, 2019Jan 25, 2019

    • psviewer

      Public
      Pre-stitched viewer of light sheet images
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 17, 2018Dec 17, 2018