Repositories list

• AMP_evasion_PDE_model

  Public
  A computational model for simulating molecular host-pathogen interactions and specifically pathogen antimicrobial peptides evasion.

  C++

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• hABM-AlveolusModel-v2

  Public
  A computational model for simulating the early innate immune defense against the human-pathogenic fungus Aspergillus fumigatus in one human alveolus

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• jipipe

  Public
  Java Image Processing Pipeline (JIPipe) is a graphical batch processing language for the ImageJ ecosystem

  Java

  •

  MIT License

  •2•13•0•4•Updated Oct 21, 2024Oct 21, 2024

• misa-framework

  Public
  Website & downloads repository of MISA++

  HTML

  •2•2•0•10•Updated Jun 18, 2024Jun 18, 2024

• JIPipe-Repositories

  Public
  Default repositories for JIPipe

  0•0•0•0•Updated May 22, 2024May 22, 2024

• Nissle-binding

  Public
  Other

  •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024

• jipipe-launcher

  Public archive
  Launcher application for JIPipe

  Java

  •

  MIT License

  •0•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• jipipe-installer-windows

  Public archive
  Windows installer for the JIPipe Launcher

  C#

  •

  MIT License

  •0•0•0•0•Updated Mar 12, 2024Mar 12, 2024

• klebsiella-rna-rna-interactome

  Public
  Code for the paper "The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division" by Ruhland et al

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Feb 7, 2024Feb 7, 2024

• MRP2_analysis_liver_confocal

  Public
  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Dec 21, 2023Dec 21, 2023

• SaAbCoInfection

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 13, 2023Dec 13, 2023

• CandidalysinModel

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Dec 11, 2023Dec 11, 2023

• Bloodi-2.0

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

• python3-snakemake-deconvolve-rif

  Public archive
  Simulates deconvolution

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•1•Updated Oct 4, 2023Oct 4, 2023

• python3-snakemake-segment-glomeruli

  Public archive
  Python 3 snakemake implementation of the glomeruli segmentation algorithm published by Klingberg et al. 2017

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•1•Updated Oct 4, 2023Oct 4, 2023

• python3-snakemake-microbench

  Public archive
  Runs common image processing algorithms on the input data

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Oct 4, 2023Oct 4, 2023

• python3-snakemake-segment-cells

  Public archive
  Segments cells with a distance transform watershed method

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•1•Updated Oct 4, 2023Oct 4, 2023

• FH_Computations

  Public
  An advanced Monte Carlo simulation framework to estimate the distribution of binding units' positions for Factor H and FHR-1 through stochastic processes.

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

• sheepfat

  Public
  IMFSegNet: cost-effective and objective quantification of intramuscular fat in histological sections by deep learning

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •1•1•0•0•Updated Aug 8, 2023Aug 8, 2023

• hABM-AlveolusModel

  Public
  A computational model for simulating early fungal infection scenarios in the human or murine alveolus.

  C++

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Aug 4, 2023Aug 4, 2023

• jipipe-python

  Public
  Adapter library for the communication between JIPipe and Python

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Jul 10, 2023Jul 10, 2023

• misa-imagej

  Public
  ImageJ plugin that provides a graphical user interface for any MISA++ module

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

• Peroxisome_HMM

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 31, 2023May 31, 2023

• jipipe-website

  Public archive
  Website project for JIPipe

  HTML

  •0•0•0•0•Updated Jan 9, 2023Jan 9, 2023

• SrfAC

  Public
  Other

  •0•0•0•0•Updated Aug 31, 2022Aug 31, 2022

• imglib2-segment-cells

  Public
  Segments cells with a distance transform watershed

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated May 20, 2022May 20, 2022

• java-imglib2-deconvolve-rif

  Public
  Deconvolution simulation example

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated May 20, 2022May 20, 2022

• imglib2-segment-glomeruli

  Public
  ImgLib2 implementation of the glomeruli segmentation published by Klingberg et al. 2017

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated May 20, 2022May 20, 2022

• java-imglib2-microbench

  Public
  Benchmark for common image processing algorithms

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated May 20, 2022May 20, 2022

• imagej.github.io

  Public
  The ImageJ wiki

  JavaScript

  •

  Other

  •123•0•0•0•Updated May 9, 2022May 9, 2022