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    20 repositories

    • Cell_ACDC

      Public
      A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •30•196•60•11•Updated May 28, 2026May 28, 2026

    • SpotMAX

      Public
      SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•14•0•0•Updated May 21, 2026May 21, 2026

    • SpotMAX_benchmark

      Public
      Scripts used to benchmark SpotMAX against other SOTA tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 8, 2026May 8, 2026

    • Cell_ACDC_installer

      Public
      Used to create a installer for Cell-ACDC
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•1•0•Updated Mar 16, 2026Mar 16, 2026

    • Cell_ACDC_Tianyi

      Public
      A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •30•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • yeast_mito_segregation_with_growth_rate

      Public
      Simulation and data analysis tools for inheritance of mitochondrial nucleoids in baker's yeast - Modified to take into account growth rate
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • Fzo1Model

      Public
      Mitochondrial inheritance model used in Dengler et al
      MATLAB
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • python-javabridge-windows

      Public
      Pre-compiled python-javabridge for Windows. Microsoft Visual C++ NOT required.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Feb 12, 2025Feb 12, 2025

    • cellpose_retraining

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •624•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • ChatziFISH

      Public
      Source code used to analyse smFISH data in Chatzitheodoridou et al. 2024
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • Cell_ACDC_Timon

      Public
      A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •30•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •624•0•0•0•Updated Feb 15, 2024Feb 15, 2024

    • activeInstanceSegment

      Public
      This repo contains the first steps towards my master thesis
      Python
      •1•5•0•0•Updated Oct 1, 2023Oct 1, 2023

    • python-javabridge-acdc

      Public
      Python wrapper for the Java Native Interface
      Python
      •
      Other
      •63•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • acdc_tools

      Public
      Collection of tools (widgets, utils, io functions, etc.) used by Cell-ACDC and spotMAX
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Jun 26, 2023Jun 26, 2023

    • SeelMito

      Public
      Python code used to analyse the microscopy data in Seel et al. 2023
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated May 2, 2023May 2, 2023

    • WinterSchool23

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 15, 2023Mar 15, 2023

    • java_portable_linux

      Public
      Portable Java 8 for Linux. Used for Cell-ACDC software to run BioFormats in Python
      Roff
      •0•0•0•0•Updated Feb 17, 2022Feb 17, 2022

    • java_portable_macos

      Public
      Portable Java 8 for macOS. Used for Cell-ACDC software to run BioFormats in Python
      Roff
      •0•0•0•0•Updated Feb 17, 2022Feb 17, 2022

    • java_portable_windows

      Public
      Portable Java 8 and JDK 8 for Windows. Used for Cell-ACDC software to run BioFormats in Python
      C
      •1•7•0•0•Updated Feb 17, 2022Feb 17, 2022
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