Murphy Lab

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44 repositories

SPRM-RRA
Public
Reproducable Research Archive for SPRM manuscript
Python
•0•0•0•0•Updated Dec 20, 2025Dec 20, 2025
SPRM
Public
Python
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GNU General Public License v3.0
•0•0•6•0•Updated Oct 2, 2025Oct 2, 2025
CellSegmentationEvaluator
Public
Evaluating the quality of a cell segmentation method without reference.
Python
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MIT License
•3•13•2•1•Updated Jul 26, 2025Jul 26, 2025
3DCellComposer
Public
3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation
Python
•
GNU General Public License v3.0
•1•3•1•0•Updated Jul 8, 2025Jul 8, 2025
ChenMurphyCytoSpatioRRA
Public
This is the reproducible research archive that reproduces all results and figures in the manuscript "CytoSpatio: Learning cell type spatial relationships using …
R
•
Other
•0•1•0•0•Updated Jun 16, 2025Jun 16, 2025
CytoSpatio
Public
CytoSpatio: Learning Cell Type Spatial Relationships
Jupyter Notebook
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Other
•1•2•1•0•Updated Apr 3, 2025Apr 3, 2025
ChenMurphy3DCellComposerRRA
Public
This is the reproducible research archive that reproduces all results and figures in the manuscript "3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Seg…
Python
•
MIT License
•0•0•0•0•Updated Aug 8, 2024Aug 8, 2024
CODEXPanelOptimization
Public
Jupyter Notebook
•0•1•0•0•Updated Jun 25, 2024Jun 25, 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
cellorganizer
Public
Repository for CellOrganizer v2.6 and above.
MATLAB
•
GNU General Public License v3.0
•4•4•7•0•Updated Jul 26, 2023Jul 26, 2023
docker-cellorganizer-jupyter-notebook
Public
CellOrganizer on Jupyter Notebook
docker modeling virtualization
docker modeling virtualization container bioimage-informatics cellorganizer
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
python docker
python docker
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
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MIT License
•1•0•0•0•Updated Nov 30, 2022Nov 30, 2022
cellorganizer-documentation_old
Public
Python
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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 …
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
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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
:whale: Script to build a Singularity image for CellOrganizer
virtualization container modeling-tools
virtualization container modeling-tools bioimage-informatics cellorganizer
Shell
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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-extraction slic location-proteomics
feature-extraction slic location-proteomics
HTML
•0•0•0•0•Updated Nov 8, 2019Nov 8, 2019
docker-matlabmcr2018b-jupyter
Public
:whale: Matlab MCR 2018b + Jupyter Notebook
docker matlab docker-image
docker matlab docker-image jupyter-notebook matlab-mcr
Dockerfile
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GNU Lesser General Public License v3.0
•0•3•1•0•Updated Oct 2, 2019Oct 2, 2019
docker-matlabmcr2017a
Public
:whale: Matlab MCR 2017a
docker matlab docker-image
docker matlab docker-image matlab-mcr
Dockerfile
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GNU Lesser General Public License v3.0
•0•0•0•0•Updated Sep 17, 2019Sep 17, 2019
docker-cellorganizer
Public
CellOrganizer for Docker
docker virtualization container
docker virtualization container modelling bioimage-informatics cellorganizer
Dockerfile
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GNU Lesser General Public License v3.0
•1•2•0•0•Updated Sep 13, 2019Sep 13, 2019
docker-matlabmcr2018b
Public
:whale: Matlab MCR 2018b
docker matlab matlab-mcr
docker matlab matlab-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
cell-modeling
MATLAB
•
GNU General Public License v3.0
•1•1•0•0•Updated Jun 20, 2019Jun 20, 2019