FAQ
BigNeuron Launch
FAQs
Updated 3.13.2015
Summary:
BigNeuron is a community effort to define and advance state-of-the-art of single neuron reconstruction: an
essential unsolved challenge in brain science. The project will both standardize the methods to generate high
quality and consistent data, and mobilize the reconstruction community to generate interest in solving these
complex and interesting algorithmic problems.
Topline Messages:
 BigNeuron will bench-test on a common open platform as many open-source, automated neuron
reconstruction algorithms as possible, using very large scale, publicly available single 3D neuron
image datasets acquired by several light microscopy methods.
 The bench-test results will be produced using some of the fastest supercomputers in the world and
then compared and validated using multiple criteria carefully defined by the computational
neuroscience community.
 The major results of BigNeuron will include:
o a worldwide community-oriented and large single neuron morphology database,
o a large set of open-source, community-based novel tools for neuroscience studies,
o a standardized protocol and resource for any future scientists to study and reconstruct neuron
morphology, and
o a rich library of morphology feature definitions and algorithms to provide the basis of quality
metrics and classification.
 The Allen Institute for Brain Science is the main driver behind this international community effort.
Key Facts:
 Scientific spokesperson: Hanchuan Peng, Ph.D.
 Other spokespersons: Christof Koch, Ph.D., Jane Roskams, Ph.D.
 Organizations involved in the collaboration (see below for more details):
o Allen Institute for Brain Science (USA)
o Janelia Research Campus (HHMI) (USA)
o Oak Ridge National Laboratory (USA)
o Lawrence Berkeley National Laboratory (USA)
o Human Brain Project (Europe)
o University of Cambridge (UK)
o Wellcome Trust (UK)
o NeuroMorpho.org and George Mason University (USA)
o Web Intelligence Consortium and Brain Informatics conferences (Japan/China)
o FlyCircuit.org (Taiwan)
o Erasmus University Medical Center (Netherlands)
MARCH 2015
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BIGNEURON LAUNCH
General Q&A
What is BigNeuron?
BigNeuron is a large-scale community project. The major goal of BigNeuron is to bench-test as many as
possible open source, automated neuron reconstruction algorithms on a common and open platform for very
large scale, single 3D neuron image datasets acquired using multi-modalities of light microscopy methods.
The bench-test results will be produced using some of the fastest supercomputers in the world and then
compared and validated using multiple criteria carefully defined by the computational neuroscience
community.
Why do we need BigNeuron?
The three-dimensional shape of a neuron plays a major role in determining its connectivity, integration of
synaptic input and cellular firing properties, and changes dynamically with its activity and state of the
organism. Analyzing the 3D morphology of neurons in an unbiased way is critical to understand neuronal
function, and developing applications to model circuitry.
Although advances in brain cellular imaging have yielded thousands of detailed images, there are no
standards to collect and compare the data. BigNeuron aims to create those standards and determine which
analysis approach is the most effective for the important questions driving the field.
Who is involved in BigNeuron, and what are their roles?
 Allen Institute for Brain Science (USA)
o Initialize and lead the project. Will coordinate the main effort, contribute neuron reconstruction
algorithms and neuron data, sponsor and host the annotation workshop, lead data analysis
and distribution effort.
 Janelia Research Campus (HHMI) (USA)
o Partner of the project. Will enable development of the Vaa3D platform and many tools,
contribution of neuron reconstruction algorithms and neuron data, sponsor and host the
USA/Canada hackathon.
 Oak Ridge National Laboratory (USA)
o Partner of the project. Will provide the major supercomputing facility.
 Lawrence Berkeley National Laboratory (USA)
o Partner of the project. Will provide some supercomputing facilities, potential data hosting (via
CRCNS.org at Berkeley) and website support.
 Human Brain Project (Europe)
o Partner of the project. Co-sponsor of the Europe hackathon at Cambridge. Will provide some
supercomputing facilities and contribute to data analysis.
 University of Cambridge (UK)
o The neuroscience department (PDN) and advanced imaging center will host the Cambridge
hackathon.
 Wellcome Trust (UK)
o Partner of the project. Will co-sponsor the Europe hackathon at Cambridge.
 NeuroMorpho.org and George Mason University (USA)
o Partner of the project. Home institute of one of the main co-organizers (Giorgio Ascoli) for
project planning, will contribute to data analysis, potentially host reconstruction data
 Web Intelligence Consortium and Brain Informatics conferences (Japan/China)
o Sponsor and host for the Asia/Australia hackathon, contribution of a neuron reconstruction
algorithm.
 FlyCircuit.org (Taiwan)
o One of the main test data contributors, may also contribute one neuron reconstruction method
 Erasmus University Medical Center (Netherlands)
o Home institute of one of the co-organizers (Erik Meijering) who will participate in data analysis
after bench testing and potentially also contribute one reconstruction algorithm.
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What will be the outcome of BigNeuron?
The major anticipated results of the project are:
 a world-wide community-oriented and large single neuron morphology database;
 a large set of open-source, community-based novel tools for neuroscience studies;
 a standardized protocol and resource for any future scientists who want to study neuron anatomy and
neuron morphology reconstructions;
 a rich library of morphology feature definitions and algorithms to provide the basis of quality metrics
and classification.
How will BigNeuron help advance brain research worldwide?
BigNeuron will ultimately provide several key resources for scientists around the world.
 A clear definition of which algorithms are most useful to analyze different types of neurons, saving
time and allowing researchers even in disparate locations to effectively compare their results.
 Standardized protocols so that researchers in different labs can reliably reproduce their results,
making for more robust and meaningful data.
 A rich library of images that scientists can draw on for their own investigations.
By creating clear standards, processes and metrics for digital reconstruction of single neurons, BigNeuron will
foster collaboration and accelerate the pace of research into single neuron morphologies around the world.
What are the project phases of BigNeuron?
 In Phase I (2015) of the project, a series of hackathons will be held in Beijing, Cambridge, and Janelia
Research Campus (HHMI), cosponsored by a range of organizations. Neuron reconstruction
algorithms contributed from participants will be ported onto a common software platform to analyze
neuronal physical structure using the same core dataset. Additional 3D images will be solicited
internationally at this time from multiple organisms.
 In Phase II (2015-2016), all ported algorithms will be bench-tested at DOE (USA) and human brain
project supercomputing centers, allowing us to standardize optimal protocols for labeling, visualizing
and analyzing neuronal structure and key biological features. Computational annotation and analysis
workshops will also be held at the Allen Institute (Seattle), Broad Institute (MIT) and in other ways, to
help analyze the performance of neuron reconstruction.
 In Phase III (2016-) the combined results of Phase I and II will be used to develop a comprehensive
annotated database of complex neuronal morphology, generate a searchable tool for discovering
annotated and unique characteristics of neuronal morphology, and lay the groundwork for potential
integrating this with large-scale datasets linking form to neuronal function.
What is the relationship between BigNeuron and Neurodata Without Borders?
Both projects are aimed at creating standards for data collection and analysis, but that they address different
issues. Neurodata Without Borders is a more general initiative, while BigNeuron is specifically about 3D
neural reconstructions. BigNeuron also has a significant data-sharing component, since images from many
different labs will be collected to create a database that researchers can access, along with the results of
algorithm bench testing.
What kind of data will BigNeuron use? What types of algorithms?
The set of BigNeuron bench-test data will include neuron image stacks from different species (including fruit
fly and other insects, fish, turtle, chicken, mouse, rat, and human) and nervous system regions such as
cortical and subcortical areas, retina, and peripheral nervous system. The test data will be from multiple light
microscopy modalities, especially laser scanning microscopy (confocal/2p) and brightfield or epi-fluorescent
imaging.
Reconstruction visualization will be supported by Vaa3D, an open-source, cross-platform system for
visualization and analysis. All algorithms to be bench tested must be ported into the Vaa3D platform.
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BIGNEURON LAUNCH
What are the hackathons?
The planned hackathons will help contributors and developers port data and algorithms onto the common
Vaa3D platform. Each hackathon will be one week long and largely focused on linking existing algorithms as
executable Vaa3D plugins.
Is BigNeuron a crowd-sourcing project?
BigNeuron is a community project, but not a crowd-sourcing project. We are not asking people to annotate
reconstructions. Instead, we ask developers and trained experts to provide different neuron reconstruction
algorithms and available manual tracing and to join in for bench-testing and analysis in a collaborative and
professional spirit. In the next phases of BigNeuron, there will be a crowd-sourcing and annotation
component, to build the reference database as comprehensively as we can.
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