HBP Neuron Morphology Viewer

Select neuron from my computer NeuroMorpho.org Allen Cell Types HBP Model Catalog

No morphology loaded.
Supported file formats: SWC, neurolucida-ASC, neurolucida-XML or neurolucida-DAT/NRX.
Use the above button to select a neuron, or try one of the samples:

c10861.CNG.swc from the Amaral lab, downloaded from neuromorpho.org
TCneuron_EP36-S1_9-9-17.DAT, thalamocortical projection neuron from the Francisco Clascá lab

Introduction

Welcome to the HBP Neuron Morphology Viewer. With this tool you can

1. Load a neuron morphology in the viewer

Supported file formats are SWC and Neurolucida (DAT,ASC,XML,NRX).
Directly access the online databases NeuroMorpho.org, Allen Cell Types, and HBP Model Catalog.
Send neuron morphologies directly from your own website or from a Jupyter Notebook.

2. View, edit and spatially register the neuron

Inspect the neuron by looking at the data points and properties as a tree, or at its 3d rendering with various configuration options.
Switch on/off parts of the neuron via the check-boxes in the data tree.
View the neuron inside a brain atlas via the Scalable Brain Atlas Composer ('View neuron in context' button).
Position the neuron in a brain atlas with the corresponding point pair tool of the Scalable Brain Atlas Composer.

3. Save the neuron as an image or morphology file

Save either the complete neuron or the selected components to SWC+ or Neurolucida (XML only) format.
Save the 3d rendering as an image, as an SVG vector file (2D) or as an XML vector file (3d).

Terms of use

The viewer is created by Rembrandt Bakker, Radboud University Nijmegen & Jülich Research Institute, 2016-2019.
If you use the morphology viewer for your research, then cite the morphology viewer publication in your publications. A manuscript is in preparation, the current citation is the following CNS abstract:
Bakker R, García-Amado M, Evangelio M, Clascá F, Tiesinga P (2017) "P271 Workflow, data format and tools to register neuron morphologies to a reference brain atlas." https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0372-1.

Acknowledgements

The viewer was developed with funding from the Human Brain Project Neuroinformatics Platform and FLAG-ERA project FIIND.

A helpful resourse in parsing Neurolucida DAT files was: Neuronland.
Inspiration also came from these other WebGL-based morphology viewers:

Shark Viewer, view on github
MPDL SWC-service (based on Shark Viewer), view on github
The Mouselight neuron browser

Feedback

If you have a particular neuron that doesn't load well, please send us (a link to) it.
If the tool does not work on a particular browser/operating system, but that combination does support x3dom (check), then check if you have any javascript errors and send us the error.
You are also welcome to submit bugs and send feature requests.

Additional functionality may be available at the development release of the viewer.

Development release only below this line

Feature requests

Show a scale-bar alongside the rendered neuron.

Playground