README.md

MouseLight Showcase cells in NeuroML2 format

A number of the cellular reconstructions from the Janelia MouseLight project have been converted to NeuroML format and can be visualised on OSB.

The original data were made available by the Janelia MouseLight project under the CC-BY NC license, https://creativecommons.org/licenses/by-nc/4.0/legalcode.

The script to perform the transformation of the downloaded JSON files is export.py and uses libNeuroML.

To use this script:

pip install libNeuroML
git clone https://github.com/OpenSourceBrain/MouseLightShowcase.git
cd MouseLightShowcase/JSON
python export.py

NOTE: cells have been given a spherical soma for visualisation purposes. However, no soma has been reconstructed from the original cells.

The cells which have been converted so far include:

AA0289

Cell with 2886 segments (soma: 1 dend: 792, axon 2093)

https://doi.org/10.25378/janelia.5527822 - NeuroML file

AA0274

Cell with 14391 segments (soma: 1 dend: 799, axon 13591)

https://doi.org/10.25378/janelia.5527774 - NeuroML file

AA0267

Cell with 38635 segments (soma: 1 dend: 389, axon 38245)

https://doi.org/10.25378/janelia.5527747 - NeuroML file

AA0261

Cell with 4960 segments (soma: 1 dend: 654, axon 4305)

https://doi.org/10.25378/janelia.5527717 - NeuroML file

AA0250

Cell with 5305 segments (soma: 1 dend: 655, axon 4649)

https://doi.org/10.25378/janelia.5527678 - NeuroML file

AA0188

Cell with 2118 segments (soma: 1 dend: 242, axon 1875)

https://doi.org/10.25378/janelia.5527468 - NeuroML file

AA0182

Cell with 2932 segments (soma: 1 dend: 339, axon 2592)

https://doi.org/10.25378/janelia.5527447 - NeuroML file

AA0180

Cell with 3849 segments (soma: 1 dend: 533, axon 3315)

https://doi.org/10.25378/janelia.5527441 - NeuroML file

AA0052

Cell with 4086 segments (soma: 1 dend: 808, axon 3277)

https://doi.org/10.25378/janelia.5521753 - NeuroML file

AA0257

Cell with 5108 segments (soma: 1 dend: 468, axon 4639)

https://doi.org/10.25378/janelia.5527702 - NeuroML file

AA0252

Cell with 4694 segments (soma: 1 dend: 418, axon 4275)

https://doi.org/10.25378/janelia.5527684 - NeuroML file

AA0248

Cell with 4316 segments (soma: 1 dend: 448, axon 3867)

https://doi.org/10.25378/janelia.5527672 - NeuroML file

AA0173

Cell with 850 segments (soma: 1 dend: 273, axon 576)

https://doi.org/10.25378/janelia.5527420 - NeuroML file

AA0171

Cell with 998 segments (soma: 1 dend: 210, axon 787)

https://doi.org/10.25378/janelia.5527414 - NeuroML file

AA0158

Cell with 1042 segments (soma: 1 dend: 287, axon 754)

https://doi.org/10.25378/janelia.5527369 - NeuroML file

AA0157

Cell with 1365 segments (soma: 1 dend: 298, axon 1066)

https://doi.org/10.25378/janelia.5527366 - NeuroML file

AA1506

Cell with 3275 segments (soma: 1 dend: 1296, axon 1978)

No DOI - NeuroML file

AA1507

Cell with 1915 segments (soma: 1 dend: 298, axon 1616)

No DOI - NeuroML file