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    54 repositories

    • 3DCellSimulationsElectricalStimulation

      Public
      We present an open-source workflow that converts 3D microscopy masks into finite-element-ready meshes for electric field simulations. The pipeline runs efficien…
      Python
      •
      Other
      •0•0•0•0•Updated May 3, 2026May 3, 2026

    • OSS-DBSv2

      Public
      Open-Source Simulation platform for Deep Brain Stimulation
      Python
      •
      GNU General Public License v3.0
      •9•18•1•3•Updated May 2, 2026May 2, 2026

    • INF-Dockerfiles

      Public
      This is a collection of Dockerfiles used in the CRC ELAINE
      Dockerfile
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • readCzi

      Public
      readCzi is an R package to read Carl Zeiss Image (CZI) files, convert them to tifs and store metadata
      R
      •
      GNU General Public License v3.0
      •1•4•1•0•Updated Mar 4, 2026Mar 4, 2026

    • Ca-imaging-RO-Crate

      Public
      RO-Crate bundles from Calcium Imaging experiments including research data and their retrospective provenance
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•3•0•0•Updated Jan 20, 2026Jan 20, 2026

    • STELLA

      Public
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • oscilloscopeR

      Public
      R package to work with oscilloscope recordings.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • detectCilia

      Public
      R package to detect cilia and other colored structures in confocal fluorescence microscopy images
      R
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jun 16, 2025Jun 16, 2025

    • SI_Nrf2_NFkB_Signalling_after_Plasma_Stimulation

      Public
      R script for image analysis
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • cellPixels

      Public
      R package for statistics of fluorescence microscopy images
      R
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Oct 2, 2024Oct 2, 2024

    • SI_lengthOfPrimaryCilia

      Public
      Supporting infomation to "Influence of cultivation methods on the lengths of primary cilia"
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • OSS-DBS

      Public archive
      Open-Source Simulation platform for Deep Brain Stimulation
      Python
      •
      GNU General Public License v3.0
      •6•17•4•3•Updated Nov 28, 2023Nov 28, 2023

    • SI_Short_Stim_MG63

      Public
      Supporting information for publication on short-term stimulation of MG-63 cells
      electrical-stimulationmg-63
      electrical-stimulationmg-63
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 21, 2023Feb 21, 2023

    • WebProv

      Public
      Online Provenance Tool for Simulation Models
      Vue
      •
      GNU General Public License v3.0
      •4•3•10•16•Updated Nov 13, 2022Nov 13, 2022

    • Structure-based-ELN2LOD

      Public
      Prototype translating ELN protocols into RO-Crate bundles including the research data and a retrospective provenance representation
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Mar 8, 2022Mar 8, 2022

    • SI_Provenance_Wnt_Family

      Public
      Supporting information for publication by Budde et al. (2021)
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 11, 2021Aug 11, 2021

    • SI_Short_Stim

      Public
      Supporting information for publication on short-term stimulation of neural progenitor cells
      neural-progenitorselectrical-stimulation
      neural-progenitorselectrical-stimulation
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 4, 2021Aug 4, 2021

    • Case-Study-Neurostimulator

      Public
      Models, generated experiments, and data for the neurostimulator case study of the paper "Making Simulation Experiments Explicit and Accessible using Experiment …
      Python
      •0•0•0•0•Updated Apr 13, 2021Apr 13, 2021

    • Case-Study-Endocytosis

      Public
      Models, generated experiments, and data for the endocytosis case study of the paper "Making Simulation Experiments Explicit and Accessible using Experiment Sche…
      R
      •0•1•0•0•Updated Apr 13, 2021Apr 13, 2021

    • elabftw

      Public
      :notebook: Lab manager, experiment notebook, database for research labs
      PHP
      •
      GNU Affero General Public License v3.0
      •296•0•0•0•Updated Mar 10, 2021Mar 10, 2021

    • elabapy

      Public
      Python package to interact with eLabFTW's API
      Python
      •
      GNU General Public License v3.0
      •10•0•0•0•Updated Mar 3, 2021Mar 3, 2021

    • ckan

      Public
      CKAN is an open-source DMS (data management system) for powering data hubs and data portals. CKAN makes it easy to publish, share and use data. It powers datahu…
      Python
      •
      Other
      •2.1k•0•0•0•Updated Feb 5, 2021Feb 5, 2021

    • SI_Staehlke_MDPI_Cells

      Public
      Supporting information for paper by Staehlke et al. 2020
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 22, 2020Dec 22, 2020

    • Semantic-Modelling-CA-Imaging

      Public
      This repository contains the semantic model of an Electronic Lab Notebook (ELN) protocols of a Calcium Imaging study.
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Oct 15, 2020Oct 15, 2020

    • SI_LRP6_Endocytosis_Model

      Public
      Supporting information for paper by Haack, Budde, Uhrmacher (doi: 10.1242/jcs.243675).
      Scala
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 22, 2020Jul 22, 2020

    • elabimg

      Public
      elabftw in a docker container
      HTML
      •
      GNU Affero General Public License v3.0
      •42•0•0•0•Updated May 8, 2020May 8, 2020

    • ImageJPlugin_Count_and_measure

      Public
      Plugin for ImageJ to count and measure cells
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 20, 2020Apr 20, 2020

    • Cartilage_electromechanics

      Public
      Python script for the manuscript_____Farooqi, A.R.; Bader, R.; van Rienen, U. Numerical Study on Electromechanics in Cartilage Tissue with Respect to Its Electr…
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 9, 2020Mar 9, 2020

    • Electro-active-hydrogels

      Public
      Python script for the manuscript_____Farooqi, A.R.; Zimmermann, J.; Bader, R.; van Rienen, U. Numerical simulation of electro-active hydrogels for cartilage tis…
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 9, 2020Mar 9, 2020

    • rdmo

      Public
      A tool to support the planning, implementation, and organization of research data management.
      Python
      •
      Apache License 2.0
      •55•0•0•0•Updated Feb 24, 2020Feb 24, 2020
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