BigNeuron Events and News

A short list of recent events and news of the BigNeuron project.

• [March 31, 2017] The UltraTracer paper based on BigNeuron tools is published in Nature Methods (http://www.nature.com/nmeth/journal/v14/n4/full/nmeth.4233.html and http://biorxiv.org/content/early/2016/11/14/087726).

• [March 30, 2017] The NeuronAssembler is published in Brain Informatics (https://link.springer.com/article/10.1007/s40708-017-0063-9).

• [March 29, 2017] The M-MAST paper is published in BMC Bioinformatics by J. Wan and Ni. Zhong et al. (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1597-9)

• [Feb 5, 2017] An ensemble neuron tracer by Wang et al, is published in Neuroinformatics (http://link.springer.com/article/10.1007/s12021-017-9325-1).

• [Jan 30, 2017] The neuron tip detection paper by Liu et al was published in Pattern Recognition (http://www.sciencedirect.com/science/article/pii/S0031320317300511).

• [Nov 14, 2016] The UltraTracer paper developed out of the BigNeuron project, was online at http://biorxiv.org/content/early/2016/11/14/087726 . This paper describes the first of its kind to trace/reconstruct arbitrarily large 3D image volume (e.g. with hundreds of billions of voxels) with any base tracer, effectively!

• [Nov 12-16, 2016] BigNeuron project and a number of tools were highlighted at #sfn16, the largest neurosciences annual conference at San Diego!

• [Nov 2, 2016] The bench testing reconstructions of almost 8000 reconstructions for gold166 datasets have been released ( https://github.com/BigNeuron/Data/releases/tag/gold166_bt_v1.0 ).

• [Oct 15, 2016] BigNeuron held a special session spanning a full day at the BIH'16, Omaha. In the morning 10 short talks were presented and in the afternoon 10 live demos were shown by the BigNeuron participants.

• [May 28, 2016] BigNeuron held an exciting Big Neuroscience data workshop at Southeast University, China on May 27-28, 2016. 130+ people attended the meeting which featured a number of presentations from experts in China, Japan, Australia, Singapore, and USA.

• [May 27, 2016] BigNeuron hackathon at University of Cambridge in 2015 has led to a newly accepted paper by Paulo Castro Aguiar group in the journal Neuroinformatics. This work has the title "N3DFix: An algorithm for automatic removal of swelling artifacts in neuronal reconstructions".

• [April, 2016] BigNeuron project published a new paper on neuron reconstruction by Tom Cai's group from University of Sydney, the title of the work is "Rivulet: 3D neuron morphology tracing with iterative back-tracking" (http://link.springer.com/article/10.1007%2Fs12021-016-9302-0).

• [March 16, 2016] BigNeuron to be highlighted at APS'2016 Annual Meeting, Baltimore, USA in the session "Large Scale Neuroscience Projects". (http://meetings.aps.org/Meeting/MAR16/Session/B12)

• [Feb 24, 2016] The BigNeuron project published a new paper "Reconstructing the brain: from image stacks to neuron synthesis" (http://link.springer.com/article/10.1007%2Fs40708-016-0041-7), describing a very large scale generation and use of the BigNeuron data and tools.

• [Feb 5, 2016] The list of 31 ported algorithms in BigNeuron is released. (https://github.com/BigNeuron/BigNeuron-Wiki/wiki/Neuron-Reconstruction-Algorithms)

• [Feb 3, 2016] BigNeuron released the first set of 2000 single neuron image stacks for developing better tracing algorithms (https://github.com/BigNeuron/Data/releases/tag/data_v1.0_first2000). These datasets are fruitfly neurons and were originally from flycircuit database. The data have been standardized using the protocol (http://alleninstitute.org/bigneuron/data/) and shared with targeted developers in 2015. Now the datasets are completely open subject to the license terms at http://alleninstitute.org/bigneuron/participate/ .

• [Jan 2016] BigNeuron finished a successful visualization and analysis hackathon at Imperial College London's Data Science Institute (http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/engineering/datascienceinstitute/eventssummary/event_4-12-2015-16-35-42). 20+ people from 7 countries attended this intensive event. Event was cosponsored by ICL, HBP, and Allen Institute.

• [Jan 2016] News about the BigNeuron Visualization and Data Analysis hackathon held at the Oak Ridge National Lab, Nov 2015. https://www.olcf.ornl.gov/2016/01/05/bigneuron-hackathon-branches-out-at-olcf/

• [Jan 2016] BigNeuron accomplished bench-testing of 44 algorithms / impelementations for all datasets with gold standard and silver standard reconstructions.

• [Dec 2015] First show of BigNeuron at Nanjing, China (http://rcls.seu.edu.cn/newsread.aspx?newsid=446)

• [Dec 2015] The BigNeuron project was introduced to Shanghai, China (http://www.shu.edu.cn/Default.aspx?tabid=10470&ctl=Detail&mid=19747&Id=89563&SkinSrc=[L]Skins/SDweb/index)

• [Dec 2015] BigNeuron was highlighted in the South Korea KAIST neuroscience workshop (http://raphe.kaist.ac.kr/apctpkaist/schedule.htm)

• [Dec 2015] BigNeuron provided the bench testing results to algorithm developers for fine-tuning of parameters and neuron tracing algorithms.

• [Nov 2015] AINI'2015 featured BigNeuron talk as a keynote (http://www.neuroinf.jp/aini2015).

• [Nov 2015] BigNeuron held the first data visualization and analysis hackathon at Oak Ridge National Lab, utilizing the large display wall of supercomputing facility. (https://www.olcf.ornl.gov/2016/01/05/bigneuron-hackathon-branches-out-at-olcf/) . Event was cosponsored by INCF, ORNL, and Allen Institute.

• [Oct 2015] A Neuron Tracing algorithm workshop devoted for BigNeuron was held together in the 2015 Bioimage Informatics conference at NIST (http://www.nist.gov/itl/ssd/is/bioimage-conference-2015.cfm). 5 teams from Janelia, HHMI (USA), Allen Inst. and Univ. of Georgia (USA), Taiwan, Singapore, and Illinois (USA), presented their featured work on various neruon tracing strategies.

• [Sept 2015] The BigNeuron project was featured at Paris 2015 RDA Meeting on Infrastructure for Understanding the Human Brain (https://rd-alliance.org/plenary-meetings/sixth-plenary/programme/e-infrastructures-rda-data-intensive-science/infrastructure)

• [Sept 2015] Milestone achieved! So far about 1.6 millions of single neuron reconstructions had been produced in BigNeuron large scale bench testing on multiple supercomputers, including TITAN, RHEA, EDISON, etc, from different sites. Interested people to analyze these data should contact us asap!

• [Sept 2015] The Brain Projects featured a BigNeuron page at http://brainprojects.onair.cc/category/data/bigneuron/ .

• [Sept 2015] Hanchuan Peng highlighted the BigNeuron project in the CRCNS PI meeting at University of Washington. (https://crcns2015.wordpress.com/)

• [Sept 2015] Giorgio Ascoli was featured for his talk at BIH'2015 and involvement of BigNeuron (http://braininformatics.london/tag/bigneuron/)

• [Aug 2015] The SmartTracing paper (also ported in BigNeuron) was published in Brain Informatics (http://link.springer.com/article/10.1007%2Fs40708-015-0018-y)

• [Aug 2015] The Big Machine for BigNeuron workshop, a supercomputing workshop featured BigNeuron, was held at London (http://braininformatics.london/)

• [Aug 2015] Erik Meijering gave a feature talk on BigNeuron at the 2015 EMBC conference at Milan, Italy (http://embc.embs.org/2015/w-fd-4/)

• [July 2015] BigNeuron color separation program developed by Hanbo Chen has been used to produced 13000+ single neuron images of fruitfly brains. These data will add to the 20000 or so contributed neuron images (of different sopecies) by other labs worldwide.

• [July 2015] First data release of BigNeuron: the training datasets of 79 neurons (https://github.com/BigNeuron/BigNeuron-Wiki/wiki/Bench-Testing-and-Training-Data#training-image-data) that come with gold standard manual annotation have been distributed to algorithm developers to fine tune their methods.

• [July 2015] Bench-testing fun began!!! Zhi Zhou and Xiaoxiao Liu are crazily busy now!!!

• [July 2015] The Neuron journal published the position paper about BigNeuron project (http://www.cell.com/neuron/abstract/S0896-6273%2815%2900599-1)

• [July 2015] The Neuroinformatics journal published an editorial on BigNeuron (http://link.springer.com/article/10.1007%2Fs12021-015-9270-9)

• [June 2015] BigNeuron data annotation workshop was held at Allen Institute. Experts of many different species gathered to reconstruct single neurons and generate gold and silver datasets for evaluating automated neuron tracing algorithms. (https://www.linkedin.com/pulse/bigneuron-seattle-neuron-annotation-workshop-june-15-17-hanchuan-peng)

• [June 2015] BigNeuron held the third algorithm porting hackathon at Janelia Research Campus of HHMI, USA. 40 people attended this event! (First day: https://www.linkedin.com/pulse/bigneuron-janelia-hackathon-first-day-june-1-2015-hanchuan-peng and demo day: https://www.linkedin.com/pulse/bigneuron-janelia-hackathon-demo-day-june-5-2015-hanchuan-peng)

• [May 2015] Oak Ridge National Lab issued a news piece about BigNeuron effort (https://www.ornl.gov/news/digitizing-neurons).

• [May 2015] BigNeuron held the second algorithm porting hackathon at University of Cambridge, UK. Event was cosponsored by Wellcome Trust, University of Cambridge and Allen Institute for Brain Science. (https://www.linkedin.com/pulse/bigneuron-cambridge-hackathon-may-4-8-2015-hanchuan-peng)

• [May 2015] GEN published a news piece about BigNeuron (http://www.genengnews.com/gen-articles/brain-projects-get-researchers-thinking-big/5474/)

• [April 2015] Lawrence Berkeley National Lab issued a news piece regarding its partnership in BigNeuron (http://cs.lbl.gov/news-media/news/2015/bigneuron-unlocking-the-secrets-of-the-human-brain/)

• [April 2015] BigNeuron came to Cambridge! (http://www.neuroscience.cam.ac.uk/news/article.php?permalink=57dc178dfd)

• [March 2015] GeekWire published its interview on BigNeuron (http://www.geekwire.com/2015/allen-institute-for-brain-science-leads-project-to-reconstruct-3d-neural-images-with-supercomputers/)

• [March 2015] George Mason University issued a press release of the BigNeuron project (https://test.gmu.edu/news/1910)

• [March 2015] The BigNeuron project goes public! News from Nature (http://www.nature.com/news/neuron-encyclopaedia-fires-up-to-reveal-brain-secrets-1.17232) , Science (http://www.sciencemag.org/news/2015/03/hacking-brain-one-cell-time), NBC (http://www.nbcnews.com/science/science-news/bigneuron-project-aims-untangle-brain-cell-structure-n334251), etc have nice coverage of this project.

• [March 2015] Allen Institute issued the press release of the BigNeuron project (https://alleninstitute.org/press-release/international-initiative-launched-advance-state-art-digital-tracings-neurons)

• [March 2015] The first BigNeuron algorithm porting hackathon kicked off at Beijing. NPR reported this event (http://www.npr.org/sections/health-shots/2015/03/31/396586398/hackers-needed-to-teach-computers-to-spot-sick-brain-cells). Event snapshots are here (https://www.linkedin.com/pulse/bigneuron-beijing-hackathon-hanchuan-peng)