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<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">Dear all,</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;text-align:center;line-height:normal" align="center"><b style><span lang="EN-GB">Would you like to get the neurons in your imaging data reconstructed
and traced for free? </span></b></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;text-align:center;line-height:normal" align="center"><b style><span lang="EN-GB">Do you have data sets which are specially challenging even for the
top commercial software currently available?</span></b></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"><br>
The University of Cambridge will host the next BigNeuron Hackathon between
4th-8th of May 2015 at the Post-doc Centre, Cambridge, UK.<span style> </span>This event is part of a larger initiative,
which aims to develop a universal streamlined solution for automated cell tracing,
using the <i style>freely available</i> Vaa3D
platform. </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><b style><i style><span lang="EN-GB">You could help in this endeavour, simply by sharing
some of your data with the software developers</span></i></b><span lang="EN-GB">.
<b style><i style>In
exchange, you will receive the results of the tracing effort</i></b>. More
information about the details and conditions of data contribution can be found below
and at <a href="http://alleninstitute.org/bigneuron/data/">http://alleninstitute.org/bigneuron/data/</a>
. </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">You can find more information about the Cambridge
Hackathon below, and also about The BigNeuron project at: <a href="http://bigneuron.org">http://bigneuron.org</a><span class=""></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><b style><span lang="EN-GB">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).</span></b><span lang="EN-GB"> If you plan to do so, please
send an email to <a href="mailto:bigneuronproject@gmail.com">bigneuronproject@gmail.com</a>
to notify us in advance.<br>
<br>
Kind regards,<br>
Paloma T. Gonzalez-Bellido (PDN) <span style><span class=""><<a href="mailto:ptg25@cam.ac.uk">ptg25@cam.ac.uk</a>></span></span> and Leila Muresan
(CAIC) <span style><span class=""><<a href="mailto:lam94@cam.ac.uk">lam94@cam.ac.uk</a>></span></span>, local organizers.</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">Hanchuan Peng (Allen Institute) <<a href="mailto:hanchuanp@alleninstitute.org">hanchuanp@alleninstitute.org</a>>
,<span class=""> </span>and the BigNeuron Consortium (<a href="http://bigneuron.org">http://bigneuron.org</a>)<br style>
<br style>
</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">-----------------------------------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><b><span lang="EN-GB">Goals and Approaches</span></b><span lang="EN-GB"><br>
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 <span style><span class=""><a href="http://vaa3d.org">http://vaa3d.org</a></span></span>). </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">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.</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">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!</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB"><br>
<b>How to get involved</b><br>
If you would like to get involved, you can steer the image analysis effort by
providing relevant data for your research.<br>
<br>
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.<br>
<br>
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).<br style>
<br style>
</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-GB">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.<br>
<br style>
<br style>
</span></p>
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