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    24 repositories

    • neurocig_app

      Public
      Elixir
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • ZetaStitcher

      Public
      ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
      stitchingmicroscopyfluorescence-microscopy-imaging
      stitchingmicroscopyfluorescence-microscopy-imagingmicroscopy-imagesvolumetric-images
      Python
      •
      GNU General Public License v3.0
      •7•46•3•2•Updated Nov 13, 2025Nov 13, 2025

    • BehavTrack

      Public
      Python
      •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • Foa3D

      Public
      A tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions.
      Python
      •
      MIT License
      •1•1•0•0•Updated Aug 25, 2025Aug 25, 2025

    • BCFind

      Public
      A tool for brain cells localization from 3D microscopy images.
      Python
      •0•3•0•0•Updated Jun 19, 2025Jun 19, 2025

    • mic

      Public
      MIC (Microscopy Illumination Correction): an illumination correction tool for 3D microscopy.
      Python
      •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

    • SPIMlab

      Public
      SPIMlab is a data acquisition and control software for Light Sheet Microscopy
      C++
      •
      Other
      •3•2•0•2•Updated Apr 28, 2025Apr 28, 2025

    • OptroLab

      Public
      C++
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • postProcessing_tools

      Public
      This repository contains tools that are useful for post processing the acquired images.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • atlas_tools

      Public
      Python
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • DANDI_Interactive_Plot_Selector

      Public
      Contains python script (also jupyter notebook) to create DANDI Interactive Plot Selector HTML page.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • ij-trajectory-classifier

      Public
      This plugin segments and classify diffusion trajectories
      Java
      •
      MIT License
      •4•0•0•0•Updated May 17, 2024May 17, 2024

    • NeuCnt3D

      Public
      An unsupervised tool for multiscale soma detection and counting in microscopy volume images.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 5, 2024Apr 5, 2024

    • QtLab

      Public
      C++
      •
      Other
      •0•2•0•0•Updated Dec 5, 2023Dec 5, 2023

    • open-fast-buffered-4ch-rf-gen

      Public
      C++
      •
      MIT License
      •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • biolabtools

      Public
      Python
      •0•0•0•2•Updated Jul 6, 2023Jul 6, 2023

    • dcimg

      Public
      A Python module for accessing Hamamatsu DCIMG files
      Python
      •
      MIT License
      •3•14•0•8•Updated Jun 28, 2023Jun 28, 2023

    • SomaSegmenter

      Public
      AI-based tool for semantic segmentation of neuronal somas
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 17, 2023May 17, 2023

    • bids-utils

      Public
      Python
      •1•0•0•0•Updated Jun 29, 2022Jun 29, 2022

    • RAPID-AF

      Public
      Real-time image-based autofocus for all wide-field optical microscopy systems
      C++
      •5•12•0•0•Updated Mar 24, 2022Mar 24, 2022

    • v3d_external

      Public
      www.vaa3d.org : download the latest Binary version here https://github.com/Vaa3D/release/releases/tag/v3.200
      C++
      •
      Other
      •39•0•0•0•Updated Nov 10, 2021Nov 10, 2021

    • 2P-LSFM-align

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2021Jan 11, 2021

    • st_fibre_analysis_hbp

      Public
      A tool for fibre analysis using structure tensor analysis algorithms (HBP)
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Sep 18, 2020Sep 18, 2020

    • neuron_segmentation_model_hbp

      Public
      CNN for automatic neuron segmentation
      Python
      •0•0•0•0•Updated Apr 9, 2020Apr 9, 2020
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