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Web-based neuron morphology viewer as an aid to develop new standards for neuron morphology file formats.

Rembrandt Bakker1* and Paul H. Tiesinga2
  • 1 Jülich Research Centre, Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Germany
  • 2 Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience, Department of Neuroinformatics, Netherlands

We present a web-based neuron morphology viewer that accepts a variety of neuron morphology file formats (Neurolucida DAT/NRX/ASC/XML, SWC) and presents the resulting neuronal tree as an interactive webpage that consists of both a data-hierarchy and a 3D graphical rendering of the neuron. The viewer was created to reconcile commonly used morphology file formats into a single internal representation. The Neurolucida DAT format (MicroBrightField, Inc.) is a widely used data format across experimental labs. It is a closed source binary format and exists in several versions. A reverse-engineered file format description is available at http://neuronland.org. Data is stored as a hierarchical tree of linear segments. The SWC format (Cannon et al. 1998) stores all neurite data as a single array in which each element contains coordinates, cylinder radius, a pointer to its parent, and a neurite type index (soma, axon, dendrite, apical dendrite, etc.). In the Neurolucida software the user is free to choose the neurite names (soma or Soma or CellBody, etc.), and this causes confusion. A limitation of the SWC format on the other hand is its cylindrical representation of the cell body. For most graph-theoretic analyses this is irrelevant, and large morphology projects such as http://neuromorpho.org (Ascoli et al. 2007) and BigNeuron (Peng et al. 2015) have adopted SWC as their data-sharing standard. On the other hand, in the BlueBrain project (Markram et al. 2015), which involves reconstruction of neocortical microcircuitry at the synapse level, the Neurolucida format has been the format of choice. In its current implementation, the viewer presents neurons as close as possible to the way they are described by their file format. Our aim is to provide tools to repair morphology files that do not fit nomenclature standards. The viewer can be used with files from the user's local file-system, or it can run as part of the Human Brain Project neuroinformatics platform (NIP) and access HBP-curated neuron morphologies directly. The viewer is under active development to cater to various use cases. In the present version, parts of the neuron can be selected or hidden, and the resulting view can be exported as a 2D image in vector graphics (SVG) format to form the basis of a publication figure. Following the morphology file format meeting that is planned to precede Neuroinformatics 2016, the tool will offer an export function to standardized 3D morphology files. The open source javascript code (https://github.com/rbakker/HBP-morphology-viewer) can be used with the node-js scripting language to construct automated format conversions. The tool can be accessed as a stand-alone tool: https://neuroinformatics.nl/HBP/morphology-viewer or through the HBP collaboratory: https://collab.humanbrainproject.eu/#/collab/47/nav/4835

Figure 1
Image

Acknowledgements

Supported by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 604102 (HBP)

References

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Ascoli GA, Donohue DE, Halavi M (2007). "NeuroMorpho.Org: a central resource for neuronal morphologies." J Neurosci. 27(35):9247-51. doi: 10.1523/JNEUROSCI.2055-07.2007.

Peng H, Hawrylycz M, Roskams J, Hill S, Spruston N, Meijering E, Ascoli GA (2015). "BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images." Neuron. 87(2):252-6. doi: 10.1016/j.neuron.2015.06.036.

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Keywords: neuron morphology, web-based viewer, neurolucida, Human Brain Project, data sharing

Conference: Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016.

Presentation Type: Demo

Topic: Visualization

Citation: Bakker R and Tiesinga PH (2016). Web-based neuron morphology viewer as an aid to develop new standards for neuron morphology file formats.. Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. doi: 10.3389/conf.fninf.2016.20.00079

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Received: 04 May 2016; Published Online: 18 Jul 2016.

* Correspondence: Dr. Rembrandt Bakker, Jülich Research Centre, Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich, Germany, r.bakker@donders.ru.nl