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https://github.com/bluebrain/molsys-cell-atlas

This repository provides overwrite and validation tests for the BBP cell atlas.

https://github.com/bluebrain/molsys-cell-atlas

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (3.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

This repository provides overwrite and validation tests for the BBP cell atlas.

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 4.34 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Example of command to be run:

python validation.py \ /home/piluso/data/00allenbrainatlas/ccfv2/annotation25ccfv2combined.nrrd \ /home/piluso/data/00allenbrainatlas/1.json \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/celldensitiescorrectednissl/ \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/overallcelldensitycorrectednissl.nrrd \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/inhibitoryneurondensitieslinprogcorrectednissl/ \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/excitatorysplit \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/mtypesdensitiesprobabilitymap \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/excitatorysplittransplant/ \ /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/mtypesdensitiesprobabilitymap_transplant/

pip install setup.py

densitiesvalidation \ --annotation /home/piluso/data/00allenbrainatlas/ccfv2/annotation25ccfv2combined.nrrd \ --hierarchy /home/piluso/data/00allenbrainatlas/1.json \ --densityfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/celldensitiescorrectednissl/ \ --celldensity /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/overallcelldensitycorrectednissl.nrrd \ --inhibitorydensityfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/inhibitoryneurondensitieslinprogcorrectednissl/ \ --excitatoryMEtypesfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/excitatorysplit \ --inhibitoryMEtypesfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/mtypesdensitiesprobabilitymap \ --excitatoryMEtypestransplantfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/excitatorysplittransplant/ \ --inhibitoryMEtypestransplantfolder /gpfs/bbp.cscs.ch/home/lcristel/fixleavesonlyrootLabel/mtypesdensitiesprobabilitymaptransplant/

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2024 Blue Brain Project/EPFL

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

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  • Public event: 1
  • Push event: 1
  • Fork event: 1
Last Year
  • Public event: 1
  • Push event: 1
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Dependencies

setup.py pypi
  • pynrrd *
  • voxcell >=3.1.6