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Ben Cumming's avatar
flexible cable-based cable_cell representation (#1083)
Benjamin Cumming authored 
* Remove spherical root/soma from morphology representations and logic.
* Replace `sample_tree` with `segment_tree`, which represents sample points in pairs and allows the representation of detached branches and cable segments.
* Remove sample point properties and predicates.
* Remove `cv_policy_flag::single_root_cv` as somata with a single attached dendrite will have a representation in the morphology of a single branch.
* Remove `arb::math::{volume/area}_sphere`, which are no longer being used.
* Remove spherical root special cases from `embed_pwlin` and `place_pwlin` objects.
* Add textual representation of `mnpos` in morphology exception text.
* Rename `sample_tree_from_swc` to `segement_tree_from_swc` and remove any special casing for one point somata.
* Remove `msample` and `mbranch` types.
* Update unit tests and python wrapper to reflect the changes.
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Arbor Library

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Citing Arbor

The Arbor software can be cited via Zenodo: DOI.

Previous versions of Arbor can be cited specifically:

  • Version 0.2: DOI
  • Version 0.1: DOI

The following BibTeX entry can be used to cite Arbor:

@INPROCEEDINGS{
    paper:arbor2019,
    author={N. A. {Akar} and B. {Cumming} and V. {Karakasis} and A. {Küsters} and W. {Klijn} and A. {Peyser} and S. {Yates}},
    booktitle={2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)},
    title={{Arbor --- A Morphologically-Detailed Neural Network Simulation Library for Contemporary High-Performance Computing Architectures}},
    year={2019}, month={feb}, volume={}, number={},
    pages={274--282},
    doi={10.1109/EMPDP.2019.8671560},
    ISSN={2377-5750}}

Alternative citation formats for the paper can be downloaded here, and a preprint is available at arXiv.