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        "author": "Ben Dichter",
        "author_email": "ben.dichter@gmail.com",
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        "description": "# nwbext_simulation_output: An extension for output data of large-scale simulations\n Developed in collaboration between the Soltesz lab and the Allen Institute during [NWB Hackathon #4](https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK04_2018_Seattle/Projects/NetworkOutput) by Ben Dichter*, Kael Dai*, Aaron Milstein, Yazan Billeh, Andrew Tritt, Jean-Christophe Fillion-Robin, Anton Akhipov, Oliver Ruebel, Nicholas Cain, Kristofer Bouchard, and Ivan Soltesz\n\nThis extension defines a single NWB data type, `CompartmentSeries`, that allows you to store continuous data (e.g. membrane potential) from many compartments of many cells in a scalable way. \n\n![Image of CompartmentSeries](docs/source/_static/multicompartment_schema_1.png)\n\nThis structure stores an arbitrarily large number of cells and cellular compartments with 5 datasets. It can scale to a million or more neurons, and enables efficient parallel read and write. It is designed to handle NEURON output data and to easily interface with the SONATA format.\n\n## Guide\n### python\n#### installation\n```\npip install git+https://github.com/bendichter/simulation_output.git\n```\n\n#### usage\n```python\nfrom pynwb import NWBHDF5IO, NWBFile\nfrom datetime import datetime\nfrom nwbext_simulation_output import CompartmentSeries, Compartments\nimport numpy as np\n\n\ncompartments = Compartments()\ncompartments.add_row(number=[0, 1, 2, 3, 4], position=[0.1, 0.2, 0.3, 0.4, 0.5])\ncompartments.add_row(number=[0], position=[np.nan])\ncs = CompartmentSeries('membrane_potential', np.random.randn(10, 6),\n                       compartments=compartments,\n                       unit='V', rate=100.)\nnwbfile = NWBFile('description', 'id', datetime.now().astimezone())\nnwbfile.add_acquisition(compartments)\nnwbfile.add_acquisition(cs)\n\nwith NWBHDF5IO('test_compartment_series.nwb', 'w') as io:\n    io.write(nwbfile)\n```\n\n### MATLAB\n#### installation\n\ncommand line:\n```\ngit clone https://github.com/bendichter/nwbext_simulation_output.git\n```\n\nin matlab:\n```matlab\ngenerateExtension('/path/to/nwbext_simulation_output/nwbext_simulation_output/nwbext_simulation_output.namespace.yaml');\n```\n\n#### usage\n```matlab\n[number, number_index] = util.create_indexed_column( ...\n    {[0, 1, 2, 3, 4], 0}, '/acquisition/compartments/number');\n\n[position, position_index] = util.create_indexed_column( ...\n    {[0.1, 0.2, 0.3, 0.4, 0.5], 0}, '/acquisition/compartments/position');\n\ncompartments = types.simulation_output.Compartments( ...\n    'colnames', {'number', 'position'}, ...\n    'description', 'membrane potential from various compartments', ...\n    'id', types.core.ElementIdentifiers('data', int64(0:5)));\n\ncompartments.position = position;\ncompartments.position_index = position_index;\ncompartments.number = number;\ncompartments.number_index = number_index;\n\nmembrane_potential = types.simulation_output.CompartmentSeries( ...\n    'data', randn(10,6), ...\n    'compartments', types.untyped.SoftLink('/acquisition/compartments'), ...\n    'data_unit', 'V', ...\n    'starting_time_rate', 100., ...\n    'starting_time', 0.0);\n\nnwb.acquisition.set('compartments', compartments);\nnwb.acquisition.set('membrane_potential', membrane_potential);\n```\n\n## Talks\nBen Dichter*, Kael Dai*, Aaron Milstein, Yazan Billeh, Andrew Tritt, Jean-Christophe Fillion-Robin, Anton Akhipov, Oliver Ruebel, Nicholas Cain, Kristofer Bouchard, Ivan Soltesz. NWB extension for storing results of large-scale neural network simulations. NeuroInformatics. Montreal, Canada (2018). [video](https://www.youtube.com/watch?v=uuYQW0EE2GY).\n\n\n",
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