[Neuroinfo] BigNeuron Neuron-Image-Collection-Days at Cambridge, UK, May 4-8, 2015

Hanchuan Peng hanchuan.peng at gmail.com
Thu Apr 23 07:48:34 CEST 2015

Dear all,

*Would you like to get the neurons in your imaging data reconstructed and
traced for free? *

*Do you have data sets which are specially challenging even for the top
commercial software currently available?*

The University of Cambridge will host the next BigNeuron Hackathon between
4th-8th of May 2015 at the Post-doc Centre, Cambridge, UK.  This event is
part of a larger initiative, which aims to develop a universal streamlined
solution for automated cell tracing, using the *freely available* Vaa3D

*You could help in this endeavour, simply by sharing some of your data with
the software developers*. *In exchange, you will receive the results of the
tracing effort*. More information about the details and conditions of data
contribution can be found below and at
http://alleninstitute.org/bigneuron/data/ .

You can find more information about the Cambridge Hackathon below, and also
about The BigNeuron project at: http://bigneuron.org

*You are welcome to visit the event, provide data, discuss with the
developers, get acquainted with the software between 4th and 8th of May, in
the Post-doc Centre (16 Mill Lane, Cambridge).* If you plan to do so,
please send an email to bigneuronproject at gmail.com to notify us in advance.

Kind regards,
Paloma T. Gonzalez-Bellido (PDN) <ptg25 at cam.ac.uk> and Leila Muresan (CAIC)
<lam94 at cam.ac.uk>, local organizers.

Hanchuan Peng (Allen Institute) <hanchuanp at alleninstitute.org> , and the
BigNeuron Consortium (http://bigneuron.org)


*Goals and Approaches*
The Cambridge hackathon (part of the BigNeuron project) helps contributors
and developers to port more data and neuron tracing algorithms onto the
common Open Source Vaa3D platform (free download at http://vaa3d.org).

In previous hackathons, BigNeuron has ported 15 automated tracing
algorithms to Vaa3D. In addition, NeuronAssembler, a plugin of Vaa3d, will
reconstruct tiled regions of large image stacks separately, and then
assemble the pieces of neurons together to produce a complete large neuron
reconstruction. A number of other neuron analysis tools are also available
on the Vaa3D platform.

In BigNeuron, we plan to bench-test against tens of thousands of 3D single
neuron image stacks (or tiles thereof), for 20+ reconstruction methods.
BigNeuron will durably benefit the neuroscience community by establishing a
Big Data resource and a set of standardized novel tools for neuron
morphologies. Most importantly, because Vaa3D is freely available, you
would be helping researchers around the world, whose work may be limited by
a funding shortage. The more data sets tested, the better the bench testing
will be!

*How to get involved*
If you would like to get involved, you can steer the image analysis effort
by providing relevant data for your research.

The set of BigNeuron bench-test data will include neuron image stacks from
different species (including fruit fly and other insects, fish, turtle,
chick, mouse, rat, and human) and nervous system regions such as cortical
and subcortical areas, retina, and peripheral nervous system.

The test data will be focusing on (but not limited to) multiple light
microscopy modalities, including especially laser scanning microscopy
(confocal/2p) and brightfield or epi-fluorescent imaging. The neurons are
labeled using different methods, such as genetic labeling and
virus/dye/biocytin injection, and will span a broad range of types (e.g.
unipolar, multipolar, releasing different neurotransmitters, and with a
wide variety of electrophysiological properties).

 All these data will be shared in a primary new public web-based database.
The first preliminary BigNeuron results are expected to be released around
early 2016.
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