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    18 repositories

    • faro

      Public
      Real-time feedback control microscopy for automation of optogenetic targeting
      Jupyter Notebook
      •
      MIT License
      •4•10•0•1•Updated Apr 8, 2026Apr 8, 2026

    • apoDet

      Public
      Python
      •0•0•3•0•Updated Feb 10, 2026Feb 10, 2026

    • LITOS

      Public
      LITOS - an easy-to-use tool for optogenetic cell stimulation
      C
      •
      MIT License
      •3•5•0•0•Updated Jan 29, 2026Jan 29, 2026

    • pertzlab_mic_configs

      Public
      Config files for microscopes of the pertzlab, university of Bern
      0•2•0•0•Updated Dec 10, 2025Dec 10, 2025

    • arcos4py

      Public
      Python package to detect and analyse collective phenomena
      Jupyter Notebook
      •
      MIT License
      •2•3•0•0•Updated Dec 1, 2025Dec 1, 2025

    • ARCOS-tutorial

      Public
      A Jupyter notebook to identify collective cell signalling in raw microscopy images
      clusteringbiologyspatial-analysis
      clusteringbiologyspatial-analysisbiological-data-analysismicroscopycell-biologybioimage-analysisbioimage-toolsbioimage-infomaticsbioimage-worflows
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Oct 28, 2025Oct 28, 2025

    • CellZarr

      Public
      CellZarr is a reproducible workflow for high-content analysis of live-cell timelapse imaging, processing raw ND2 files to quantitative features for scalable bio…
      bioinformatics-pipeline
      bioinformatics-pipeline
      Jupyter Notebook
      •0•1•0•0•Updated Oct 2, 2025Oct 2, 2025

    • ARCOS

      Public
      An R package to detect collective spatio-temporal phenomena
      cluster-analysisspatio-temporal-analysistime-series-analysis
      cluster-analysisspatio-temporal-analysistime-series-analysissingle-cell-data
      R
      •
      Other
      •4•13•1•0•Updated Sep 25, 2025Sep 25, 2025

    • ARCOSpx-publication

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Sep 25, 2025Sep 25, 2025

    • arcosPx-napari

      Public
      A napari plugin to track spatio-temporal correlations in images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•0•0•Updated Sep 23, 2025Sep 23, 2025

    • arcos-gui

      Public
      napari-plugin to analyse collective signalling events
      pythoncell-signallingcollective-events
      pythoncell-signallingcollective-events
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•0•0•Updated Apr 1, 2025Apr 1, 2025

    • shiny-timecourse-inspector

      Public
      R
      •
      GNU General Public License v3.0
      •2•3•0•0•Updated May 8, 2024May 8, 2024

    • CODEX

      Public
      Convolutional Neural Network for Dynamics EXploration (CODEX) is a method for mining time-series dataset by leveraging CNN features.
      Jupyter Notebook
      •
      MIT License
      •2•6•0•0•Updated Sep 21, 2023Sep 21, 2023

    • dzPlateViewer

      Public
      Deep Zoom Plate Viewer for microscopy images
      JavaScript
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Oct 12, 2021Oct 12, 2021

    • screenQC

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 9, 2020Sep 9, 2020

    • shiny-freeclust

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 9, 2020Sep 9, 2020

    • Outlier_app

      Public
      R
      •2•0•0•0•Updated Aug 11, 2019Aug 11, 2019

    • 96ChLED

      Public
      R Script to control the 96ChLED optiogenetical plate from Life Cell Instrument
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 26, 2018Sep 26, 2018
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