The BigNeuron project aims to gather a worldwide community to define and advance the state-of-the-art of single neuron reconstruction by bench-testing many automated neuron reconstruction methods against as many neuron datasets as possible following standardized data protocols and evaluation methods.
BigNeuron will durably benefit the neuroscience community by establishing a Big Data resource and a set of standardized novel tools for neuron morphologies.
Goals and Approaches
- The hackathon (part of the BigNeuron project) helps contributors and developers to port data and algorithms onto the common Vaa3D platform, (free download at http://vaa3d.org).
- 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.
- We plan to bench-test against 30,000 to 130,000 3D single neuron image stacks (or tiles thereof), for 20~30 reconstruction methods.
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, 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 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 the end of 2015.
You are welcome to visit the event, provide data, discuss with the developpers, get acquainted with the softwareDuring the hackathon.
Organizers:
Hanchuan Peng (Allen Institute)
Paloma T. Gonzalez-Bellido and Leila Muresan (CAIC) , Local organizers.