Repositories list

• SPRM

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•6•0•Updated Oct 30, 2024Oct 30, 2024

• ChenMurphy3DCellComposerRRA

  Public
  This is the reproducible research archive that reproduces all results and figures in the manuscript "3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation"

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 8, 2024Aug 8, 2024

• SPRM-RRA

  Public
  Reproducable Research Archive for SPRM manuscript

  Python

  •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

• CODEXPanelOptimization

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jun 25, 2024Jun 25, 2024

• 3DCellComposer

  Public
  3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation

  Python

  •

  GNU General Public License v3.0

  •1•1•2•0•Updated Feb 8, 2024Feb 8, 2024

• CellSegmentationEvaluator

  Public
  Evaluating the quality of a cell segmentation method without reference.

  Python

  •

  MIT License

  •2•7•5•0•Updated Feb 8, 2024Feb 8, 2024

• phenocycler-pipeline

  Public
  Forked from celldive/mibi to create new pipeline for phenocycler

  Python

  •

  GNU General Public License v3.0

  •4•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• ChenMurphyCytoSpatioRRA

  Public
  This is the reproducible research archive that reproduces all results and figures in the manuscript "CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models".

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 7, 2023Sep 7, 2023

• CytoSpatio

  Public
  CytoSpatio: Learning Cell Type Spatial Relationships

  R

  •

  GNU General Public License v3.0

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

• cellorganizer

  Public
  Repository for CellOrganizer v2.6 and above.

  MATLAB

  •

  GNU General Public License v3.0

  •3•2•7•0•Updated Jul 26, 2023Jul 26, 2023

• docker-cellorganizer-jupyter-notebook

  Public
  CellOrganizer on Jupyter Notebook

  dockermodelingvirtualization+ 3containerbioimage-informaticscellorganizer

  Jupyter Notebook

  •1•0•7•3•Updated May 22, 2023May 22, 2023

• cellorganizer-jupyter-notebooks

  Public
  jupyter notebooks for workshop

  Jupyter Notebook

  •1•0•1•0•Updated May 15, 2023May 15, 2023

• cellorganizer-python

  Public
  Python wrapper for CellOrganizer binaries

  pythondocker

  Python

  •

  GNU General Public License v3.0

  •0•0•6•0•Updated Apr 21, 2023Apr 21, 2023

• matlabmcr2019b-jupyter

  Public
  Dockerfile

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Apr 5, 2023Apr 5, 2023

• cellorganizer-docker-images

  Public
  default image set to be used in combination with cellorganizer deployed on docker

  0•0•0•0•Updated Apr 5, 2023Apr 5, 2023

• models

  Public
  0•0•0•0•Updated Feb 20, 2023Feb 20, 2023

• TetAlyze

  Public
  MATLAB

  •0•0•0•0•Updated Dec 22, 2022Dec 22, 2022

• PearsonGroupImages

  Public
  0•0•0•0•Updated Dec 21, 2022Dec 21, 2022

• ChenMurphy2DSegEvalRRA

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Nov 30, 2022Nov 30, 2022

• cellorganizer-documentation_old

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 1, 2022Nov 1, 2022

• BioActive

  Public
  BioActive provides end-to-end capabilities for Automated Science: definition of an experimental campaign, modeling using existing data, active machine learning to select experiments, and protocols for driving laboratory automation.

  Python

  •0•0•0•0•Updated Sep 12, 2021Sep 12, 2021

• cellorganizer-galaxy-tools

  Public
  CellOrganizer tools and scripts for Galaxy Project - gitlab import

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 7, 2020Dec 7, 2020

• models2table

  Public
  MATLAB

  •0•0•0•0•Updated Dec 7, 2020Dec 7, 2020

• singularity-cellorganizer

  Public
  🐳 Script to build a Singularity image for CellOrganizer

  virtualizationcontainermodeling-tools+ 2bioimage-informaticscellorganizer

  Shell

  •

  GNU Lesser General Public License v3.0

  •0•0•4•1•Updated Apr 21, 2020Apr 21, 2020

• SLIC

  Public
  Subcellular Localization Image Classifier (SLIC)

  feature-extractionsliclocation-proteomics

  HTML

  •0•0•0•0•Updated Nov 8, 2019Nov 8, 2019

• docker-matlabmcr2018b-jupyter

  Public
  🐳 Matlab MCR 2018b + Jupyter Notebook

  dockerdocker-imagejupyter-notebook+ 2matlab-mcrmatlab

  Dockerfile

  •

  GNU Lesser General Public License v3.0

  •0•3•1•0•Updated Oct 2, 2019Oct 2, 2019

• docker-matlabmcr2017a

  Public
  🐳 Matlab MCR 2017a

  dockermatlabdocker-image+ 1matlab-mcr

  Dockerfile

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Sep 17, 2019Sep 17, 2019

• docker-cellorganizer

  Public
  CellOrganizer for Docker

  virtualizationcontainermodelling+ 3bioimage-informaticsdockercellorganizer

  Dockerfile

  •

  GNU Lesser General Public License v3.0

  •1•2•0•0•Updated Sep 13, 2019Sep 13, 2019

• docker-matlabmcr2018b

  Public
  🐳 Matlab MCR 2018b

  dockermatlabmatlab-mcr

  Dockerfile

  •

  GNU Lesser General Public License v3.0

  •0•1•1•0•Updated Sep 2, 2019Sep 2, 2019

• cellorganizer_old

  Public
  CellOrganizer public repository

  cell-modeling

  MATLAB

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Jun 20, 2019Jun 20, 2019