TREES Toolbox statistics

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Protocols

TREES Toolbox specifications

Information


Unique identifier OMICS_27978
Name TREES Toolbox
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.15
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Hermann Cuntz
  • person_outline TREES Toolbox Team
  • person_outline TREES Toolbox Team

Additional information


http://www.treestoolbox.org/manual.html

Publication for TREES Toolbox

TREES Toolbox citations

 (3)
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Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study

2018
PLoS Comput Biol
PMCID: 5862493
PMID: 29522509
DOI: 10.1371/journal.pcbi.1006027
call_split See protocol

[…] All simulations were performed in NEURON and Python []. The TREES toolbox [] was used for steady-state analysis of injected current in abstract models, and NeuroTools toolbox [] was used for spiketrain analysis. Our simulations were calibrated with experimenta […]

library_books

T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult born dentate granule cells

2017
eLife
PMCID: 5737656
PMID: 29165247
DOI: 10.7554/eLife.26517.030

[…] The programming environment Matlab (Mathworks, version 2015b, some functions of the GC model are not functional in earlier Matlab versions) was used together with the TREES toolbox to analyze raw electrophysiological data from , as well as the output of the compartmental modeling simulations. Electrophysiological properties were measured as following: The input res […]

library_books

SIDEKICK 2 DIRECTS FORMATION OF A RETINAL CIRCUIT THAT DETECTS DIFFERENTIAL MOTION

2015
Nature
PMCID: 4552609
PMID: 26287463
DOI: 10.1038/nature14682

[…] re skeletonized manually through the z-stack using simple neurite tracer (ImageJ). Path ROIs describing neuronal processes were converted to stacks and analyzed for morphological properties using the Trees toolbox. We measured the projection depth of VG3-ACs and W3B-RGCs by taking the z-axis intensity profile of labeled neurons and plotted this profile as a % of IPL depth. IPL depth in turn was de […]

Citations

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TREES Toolbox institution(s)
Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; Department of Systems and Computational Neurobiology, Max-Planck Institute of Neurobiology, Martinsried, Germany
TREES Toolbox funding source(s)
Supported by the Gatsby Charitable Foundation, the Wellcome Trust, the Alexander von Humboldt Foundation, the Max-Planck Society, and the ENI-Net.

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