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CIBB 2016 - Second Call for Papers
by Andrea Bracciali May 9, 2016

May 9, 2016

[apologies for multiple posting] ============================================================== SECOND CALL FOR PAPERS CIBB 2016 13th International Meeting on Computational Intelligence methods for Bioinformatics and Biostatistics University of Stirling, Stirling, Scotland UK September 1-3 2016 http://www.cs.stir.ac.uk/events/cibb2016/ cibb2016(a)gmail.com ============================================================== In evidence (please see below and the web for details): - the very interesting list of INVITED SPEAKERS is growing ! - five new SPECIAL SESSIONS are running ! - EXTENDED DEADLINES for paper submission Please, connect to the conference via @CIBB2016 on twitter Keynote Speakers (to be completed) Prof. Mark Beaumont School of Biological Sciences, Bristol University Evolutionary Biology Prof. Natalio Krasnogor School of Computing Science, Newcastle University Computing Science and Synthetic Biology Prof. Bud Mishra Courant Institute of Mathematical Sciences and NYU School of Medicine, New York University NYU, and Mt Sinai School of Medicine Computer Science, Cell Biology and Genetics Dr. Guido Sanguinetti School of Informatics, University of Edinburgh System design of stochastic models SPECIAL SESSIONS Engineering Bio-interfaces and Rudimentary Cells as a way to develop Synthetic Biology Contacts: Maria Raposo, mfr(a)fct.unl.pt Biocuration and integration of biomedical databases Contacts: Riccardo Rizzo, ricrizzo(a)pa.icar.cnr.it Modelling and simulation methods for Systems Biology and Systems Medicine Contacts: Paolo Cazzaniga, paolo.cazzaniga(a)unibg.it High-Performance Computing and Deep learning methods for Genomic Data Analysis Contacts: : Fabio Tordini, tordini(a)di.unito.it Statistical inference in mechanistic models of biological system Contacts: Dirk Husmeier, Dirk.Husmeier(a)glasgow.ac.uk Scope The main goal of this 13th edition of the CIBB international conference is to provide a multi-disciplinary forum open to researchers interested in the application of computational intelligence, in a broad sense, to open problems in bioinformatics, biostatistics, systems and synthetic biology and medical informatics. Cutting edge methodologies capable of accelerating life science discoveries will be discussed. Following its tradition and roots, this year's meeting will bring together researchers from the international scientific community interested in advancements and future perspectives in bioinformatics and biostatistics. Also, looking at current trends and future opportunities at the edge of computer and life sciences, the application of computational intelligence to system and synthetic biology, and the consequent impact on innovative medicine will be of great for the conference. Theoretical and experimental biologists are also invited to participate in order to present novel challenges and foster multidisciplinary collaboration. The scientific program of CIBB 2016 will include Keynote Speakers, tutorials and special sessions. Contributed papers will be presented in plenary oral sessions, special sessions, or poster sessions. Topics of interest include, but are not restricted to: · Next generation sequencing bioalgorithms · Multi-omics data analysis · High dimensional statistical analysis of omics data · Algorithms for alternative splicing analysis · Algorithms for molecular evolution and phylogenetic analysis · Methods for the visualization of high dimensional complex omic data · Software tools for bioinformatics · Methods for comparative genomics · Methods for functional classification of genes · Methods for unsupervised analysis, validation and visualization of structures discovered in bio-molecular data · Health-Informatics and Medical Informatics. · Methods for the integration of clinical and genetic data · Heterogeneous data integration and data fusion for diagnostics · Algorithms for pharmacogenomics · Biomedical text mining and imaging · Methods for diagnosis and prognosis within personalized medicine · Statistical methods for the analysis of clinical data · Prediction of secondary and tertiary protein structures · Mass spectrometry data analysis in proteomics · Algorithms for molecular evolution and phylogenetic analysis · Bio-molecular databases and data mining · Mathematical modeling and automated reasoning on biological and synthetic systems · Computational simulation of biological systems · Methods and advances in systems biology · Spatio-temporal analysis of synthetic and biological systems · Network systems biology · Models for cell populations and tissues · Methods for the engineering of synthetic components · Modelling and engineering of interacting synthetic and biological systems · Software tools for bioinformatics, biostatistics, systems and synthetic biology Publication Accepted papers will be presented at the conference (at least one author is expected to register), and will be published on proceedings for conference distribution. Extended and revised versions of the papers presented at CIBB 2016 will be invited for a post-conference monograph. This is traditionally published in the Springer series of Lecture Notes in Bioinformatics (LNBI), (arrangements undergoing). Continuing the tradition of CIBB, we are planning to publish best papers in one (or more, as appropriate) special issue of an international scientific journal (such as BMC Bioinformatics, in the latest editions). Paper Submission Papers must be prepared following the guidelines illustrated on the CIBB web site and should be long between 4 and 6 pages. Papers should be submitted in PDF format on the Easy Chair conference system (link available on the web site). Important Dates Paper submission deadline: 29th May 2016 Notification of acceptance: 22nd June 2016 Final paper due: 8th July 2016 Conference: 1st -3rd September 2016 General Chairs Andrea Bracciali, University of Stirling, UK David Gilbert, Brunel University London, UK Gilbert MacKenzie, UL, ENSAI and Keele, UK

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3-year sensory-motor learning research fellow position at University of Birmingham
by Joseph Galea (School of Psychology) May 9, 2016

May 9, 2016

Dear all, Applications are invited for a 3-year postdoctoral position with Dr. Joe Galea (http://josephgalea.weebly.com) at University of Birmingham, UK (www.birmingham.ac.uk/schools/psychology/index.aspx<http://www.birmingham.ac.uk/schools/psychology/index.aspx>). The successful candidate will work on an ERC starting grant which will build upon recent work from the lab that has shown reward and punishment-based feedback to have dissociable effects on motor learning. Using a combination of behavioural analysis, genetics, pharmacology and modelling techniques this project will provide the first in-depth behavioural and neural account of the role of motivation (reward/punishment) in motor learning. For 1st of October 2016, I am looking to appoint a highly motivated candidate for a postdoctoral position. This role is aimed at developing a set of motor learning based tasks (model-based/ reinforcement/ use-dependent) that will be used to examine motivation in a range of motor learning settings. The postholder will be responsible for the programming of these tasks, testing them in a large set of healthy volunteers (who we will also collect genetic data from) and for the analysis of the behavioural data (kinematic/computational models). The successful candidate will have a PhD in Psychology, Physiology, Neuroscience, Engineering, Physics or Maths and have extensive experience with programming and running motor control/learning studies. Ideally they will be familiar with the KINARM end-point robot (B.KIN technologies) and/or be an expert with Simulink/Matlab (graphical-based programming). An ability to analyse behavioural data with matlab and perform computational analysis would be ideal. Finally they should have evidence of good academic writing and presentation skills through conference presentations and a strong (recent) publication record. Detailed information can be found here: http://www.jobs.ac.uk/job/ANP415/research-fellow/ Informal enquiries should be directed to: Dr. Joseph Galea (j.galea(a)bham.ac.uk) Closing date: 3/June/2016 Best regards, Joseph Galea Senior Birmingham Fellow ERC Starting Grant Holder School of Psychology University of Birmingham, UK.

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First CfP SAN2016
by Manousos Klados May 8, 2016

May 8, 2016

Dear colleagues, please, accept our advanced apologies for any multiple cross-postings... The Society of Applied Neuroscience (SAN, http://www.applied-neuroscience.org/) in cooperation with the Medical School of the Aristotle University of Thessaloniki and the Department of Neurology of the Max Planck Institute for Human Cognitive and Brain Sciences, have the great pleasure to invite you to the biennial meeting of the Society, SAN2016 (http://applied-neuroscience.org/san2016/) which will be held in Corfu Island, Greece between 6-9 of October, 2016. We cordially invite everyone engaged in studies of Neuroscience, to participate in the SAN2016 meeting. Apart from the highly promising scientific program, blended with numerous workshops and special sessions, there will also be a lively social program which will give our guests the opportunity to enjoy Greece and Corfu.We feel confident than you will enjoy SAN2016 both scientifically and socially as one of our main purposes is to give the chance to all colleagues to establish new fruitful international collaborations in areas of mutual academic and clinical interests. SAN2016 will bring together scientists and practitioners from a wide range of specialist fields. These include, but are not limited to: EEG/ MEG/ fMRI/ fNIRS Neurofeedback fMRI-NFB studies Brain Computer Interfaces Trans Cranial Magnetic Stimulation Peripheral Biofeedback Direct Current Stimulation Event-Related Potentials Brain Connectivity Neuronal Reorganization EEG and Cognition QEEG Diagnosis Emerging combined EEG and Virtual/augmented reality technology Instrumentation Audio-Visual Stimulation LORETA & Methodology Clinical, educational, sport and optimal performance applications Rehabilitation Integrative Therapy Complimentary evidence-based applications ...and all fields of applied neuroscience. All the above blended by an attractive selection of keynote and invited speeches, as well as, hands-on pre-conference workshops. There will be a practitioner track focusing on topical issues. The conference committee receives more proposals than space available. Careful attention to Quality of work, clarity and completeness of the submitted materials is likely to increase the chance for acceptance. All the accepted abstracts will be published in the Frontiers in Human Neuroscience. SAN2016 abstract submission is supported by a Frontiers event and are directly submitted through the following link until the 20th of June, 2016: http://www.frontiersin.org/events/SAN2016_Meeting/3717 Numerous special issues and research topics are also planned by Society members as per tradition. We believe that SAN2016 will be a wonderful chance for you, to meet old friends and make new ones. We look forward to seeing you in Corfu, Greece! Panos Bamidis John Gruzelier Manousos Klados SAN2016 Conference Chairs Manousos Klados, PhD Max Planck Institute for Human Cognitive & Brain Sciences Research Group of Neuroanatomy and Connectivity Phone: +49(0)-341-9940-2507 <+49(0)-341-9940-2507> Mobile: +49(0)-176-6988-1781 Email: klados(a)cbs.mpg.de <klados(a)cbs.mpg.de> Website: http://www.mklados.com Skype: mklados | Twitter: @mklados Address: Stephanstraße 1a PC D-04103 Leipzig Germany Join us at our next event:SAN 2016 Conferece <http://applied-neuroscience.org/san2016/index.php>

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Research Position: Brain Prosthesis Algorithms
by Randal Koene May 6, 2016

May 6, 2016

Brain Prosthesis Algorithms Brain science is the new rocket science. We’re building algorithms and software to correct deficits and enhance cognitive brain function using electrophysiology. We’re not making drugs or creating a brain training game, we’re using a data driven method to create neural prostheses to restore and enhance human cognitive performance. Join us in this delicious engineering opportunity in developing probabilistic kernel models of the hippocampus for a first application in memory. What we’re looking for: a data & algorithms or machine learning specialist with an exceptional aptitude for regularization and matrix algebra. Potential projects include building classification and regression models for neural spiking data, decoding of the spatio-temporal patterns of spikes with respect to behavior, analyzing large-scale complex neural data, building mixed model of point-process signals, and other data-driven modeling projects. Working with the cross-disciplinary members of our team which includes Professors at the University of Southern California (USC), you would be driving a neural system identification modeling platform that is pushing the state-of-the-art in neurocognitive therapeutics. Self-taught or via formal education, we expect not only that you meet our prerequisites on skills and mission alignment, but that you thrive in a meritocracy of mutual peer review within a first-class team. We expect that you take responsibility for your projects, demonstrate excellence, vision, and diligent but creative invention. You are the right person for this job if you are: - Strong in linear algebra/matrices, basis transformations, model order / dimension reduction, numerical methods - Strong in regression analysis, data analysis, nonlinear mathematical modeling - Results oriented, driven, flexible, adaptable, and have the courage to take on an ambitious project, because what matters most is to build a flourishing future We’d also love it if you have skills and experience in: - Either electrical engineering, biomedical engineering, statistics, computer science, computational neuroscience, or related fields - Machine learning (e.g. Bayesian, deep learning), time series analysis, pattern recognition, and point-process signal processing is highly preferred - Neural circuit modeling / exploration (e.g. discovering functional connectivity), control theory, system identification, compartmental neural modeling (e.g. NEURON) - Python, Matlab, C/C++/C#, R, Linux/Unix Exceptional team. Full-time. Benefits. Competitive compensation. Ground breaking work. To apply, please send an email with 1) CV (and list of publications) and 2) contact information for 2-3 professional references to: Dr. Randal A. Koene at brainprosthesis(a)gmail.com with a subject line “Brain Prosthesis Algorithms application”.

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Postdoctoral Research Assistant in functional optical neuroimaging (fNIRS) interpretation
by f.orihuela-espina＠ccc.inaoep.mx May 6, 2016

May 6, 2016

Please disseminate as appropriate and apologies for duplicates *Postdoctoral Research Assistant in functional optical neuroimaging (fNIRS) interpretation* Publication date: 30-Dec-2015; Revised: 1-May-2016 *About the Position*: The Department of Computer Science at Instituto Nacional de Astrofísica, Óptica y Electrónica (INAOE) in Puebla, Mexico, invites applications for a 1.5 years full-time postdoctoral research assistant position in the field of functional optical neuroimaging (fNIRS) interpretation. The position will suit candidates with strong background in Knowledge Representation, Statistics and Experimental Design, Medical Physics and/or Neurosciences. Candidates must hold a Ph.D. in a relevant discipline (e.g. computer science, mathematics, statistics, physics, engineering, neurosciences). The position is invited as from the 1st of September 2016 but earlier or later incorporations might be considered. *About the project*: Functional near infrared spectroscopy (fNIRS) is an emerging neuroimaging modality available for understanding brain behaviour for which current analysis and interpretation methods were often inherited and adapted from other neuroimaging modalities such as functional magnetic resonance imaging (fMRI). This migration of methods is never trivial or without compromises. This 3 years $2M MXN project explores alternative analysis and interpretation algorithms and techniques specifically developed for fNIRS which can answer complex questions about cognitive activity while considering and exploiting fNIRS specific particularities. For further details about the project and how to apply, please visit: http://ccc.inaoep.mx/~f.orihuela-espina/Src/Jobs.php *Contact*: Dr. Felipe Orihuela-Espina. e-mail: f.orihuela-espina(a)ccc.inaoep.mx

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INCF short course in neuroinformatics, Aug 31 - Sep 1 in Reading, UK
by Malin Sandström May 6, 2016

May 6, 2016

Dear all, (apologies for cross-posting) This year, the two-day INCF short course in neuroinformatics will be held in Reading, UK on August 31 - September 1, just before INCF's Neuroinformatics 2016 <http://neuroinformatics2016.org/>. The course is intended for neuroscience researchers wishing to develop their interests in neuroinformatics as well as informatics researchers with a strong interest in neuroscience. The course is open to advanced students, postdoctoral researchers, and faculty members. Basic knowledge of neuroscience is a prerequisite. Apply latest May 31! https://www.incf.org/resources/training/incf-short-course-2016 *Topics covered* data analysis and neuronal coding databases and ontologies multiscale modeling neuroengineering simulation/computation/workflows visualization dynamic field theory *Speakers* David Willshaw (Edinburgh, UK) GIacomo Indiveri (Zürich, Switzerland) Hayriye Cagnan (Oxford, UK) Yulia Sandamirskaya (Zürich, Switzerland) Roberto Toro (Paris, France) Gaute Einevoll (Ås, Norway) Marja-Leena Linne (Tampere, Finland) Please help spread the word to prospective students! Best regards, Malin -- Malin Sandström, PhD Community Engagement Officer malin.sandstrom(a)incf.org International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org

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4-year Ph.D. Position in Neuroscience at the Donders Institute
by Bernhard Englitz May 5, 2016

May 5, 2016

Dear List, we are pleased to announce a 4-year Ph.D. position in the field of neuroscience, with a focus on acquisition and computational analysis of multilevel neural data. The position will be jointly supervised by Dr. Englitz and Dr. Cohen. Please find the details of the call below. Best wishes, Bernhard & Mike Bernhard Englitz, Ph.D. Assistant Professor Department of Neurophysiology Donders Centre for Neuroscience Faculty of Science, Radboud Universiteit Heyendaalseweg 135, 6525 AJ Nijmegen ------------------------------------------------------------------------------------------------------------------------------------ Project: This project will involve a combination of EEG and lowlevel neural recordings from multiple areas of the brain in rodents. Our focus will be on the rapid patterns of electrical activity that are observed during rest, sleep, and cognition. We will compare neural activity in multiple brain regions to simultaneously recorded EEG activity, in order to determine how these multiscale microstates are related to sensory processing. Results from this project will help us understand how the EEG signal is related to the complex spatiotemporal dynamics of the brain, its neural computations, and their relation to sensory perception. In turn, these findings will help lay groundwork for individualized diagnosis of brain dysfunctions. Scientific Environment: The Donders Institute for Brain, Cognition and Behaviour consists of three research centres, the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The Donders Institute focuses on state-of-the-art cognitive neuroscience, in a multidisciplinary approach, and offers excellent lab and neuroimaging facilities. The position will be jointly hosted at the Neuroinformatics and the Neurophysiology departments, which together provide a high quality neuroscience environment with facilities for chronic and non-chronic many-channel recordings, imaging and computational modeling. The research questions of the departments range from fundamental to applied, and enable the interaction of theory and experimental work in a single location. The Donders Institute is an equal opportunity employer, committed to building a culturally diverse intellectual community, and as such encourages applications from women and minorities. Radboud University offers a parental leave scheme and day care on campus. Qualifications: - MSc degree in computational neuroscience, mathematics, physics, engineering or a related area. - Experience with programming and data analysis in Matlab/Python. - Experience with quantitative analysis (e.g. linear algebra, time-frequency analysis) - Experience with electrophysiology is considered a plus. - The applicant should have a pro-active attitude, good communication skills, and be able to effectively work in a multi-disciplinary team. Application Link: http://www.ru.nl/werken/details/details_vacature_0/?recid=579059 <http://www.ru.nl/werken/details/details_vacature_0/?recid=579059> Closing Date of Call : 30.5.2016 Planned Starting Date : 1.9.2016

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Ph.D. and Master positions in theoretical neuroscience at the MPI for Brain Research
by Tatjana Tchumatchenko May 4, 2016

May 4, 2016

Ph.D. and Master positions in theoretical neuroscience at the Max Planck Institute for Brain Research We are seeking undergraduate students interested in writing a Master thesis and also have open positions for Ph.D. Students to join our group "Theory of neural dynamics" at the Max Planck Institute for Brain Research lead by Dr. Tatjana Tchumatchenko. Our group studies how networks of neurons encode and decode sensory stimuli and how these functions are related to computations that underlie cognitive functions and behavior. We develop models to address linear and non-linear properties of neuronal networks and have ongoing collaborations with experimental labs where we analyze in vitro as well as in vivo data and develop appropriate models to explain the observed phenomena. Successful applicants should have a strong background in a quantitative field such as physics, mathematics or computer science and should be interested in an interdisciplinary exchange with other disciplines such as biology or medicine. Life science majors interested in quantitative modeling work are also encouraged to apply, particularly if they would like to combine experiments and theory in their Master or Ph.D. thesis work. We are looking for candidates with strong English skills and prior programming experience. In order to make teamwork in our group enjoyable and fun, the ideal candidate should have a strong work ethic and have demonstrated consistent self-motivation skills. Female students are particularly encouraged to apply. Prospective students should apply by sending an email to theoryneuraldynamics(a)gmail.com which includes * a letter of motivation, * CV, * and a copy of the current academic transcripts To make your motivation letter easier to write for you and more informative for us, please check the list of questions to be answered in your motivation letter at http://www.tchumatchenko.de/Opportunities.html Looking forward to your applications! Tatjana Tchumatchenko -- Dr. Tatjana Tchumatchenko Research group leader Theory of Neural Dynamics Max Planck Institute for Brain Research Max-von-Laue-Str 4 60438 Frankfurt am Main, Germany www.tchumatchenko.de

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Collaborative Development of Data-Driven Models of Neural Systems: Janelia Farm Sept 18-12
by Padraig Gleeson May 4, 2016

May 4, 2016

[Apology for cross-postings] Dear colleagues, We are pleased to announce a conference on: Collaborative Development of Data-Driven Models of Neural Systems September 18-21, 2016 Janelia Farm Research Campus, Virginia, USA Deadline for registration: 18th May Detailed computational models are critical for elucidating neuronal and network function. They enable different levels of description to be linked, a wide range of neurophysiological experiments to be interpreted and quantitative predictions to be made. These factors are important for understanding large-scale complex systems, like neural circuits; however, more extensive use and scaling up of these data driven models pose challenges in ensuring that models are scientifically rigorous, as well as accessible and usable by both theoretical and experimental researchers alike. This conference will bring together a range of experimentalists, theoreticians and neuroinformatics developers with the aim of facilitating a global, open infrastructure for collaborative model development in neuroscience. *Organizers* Padraig Gleeson, University College London Angus Silver, University College London *Invited Participants* Anton Arkipov, Allen Institute for Brain Science Giorgio Ascoli, George Mason University Upinder Bhalla, National Centre for Biological Sciences Avrama Blackwell, George Mason University Kevin Briggman, National Institute of Neurological Disorders and Stroke/NIH Dean Buonomano, University of California, Los Angeles Nicholas Cain, Allen Institute for Brain Science Claudia Clopath, Imperial College London Rosa Cossart, Institut de Neurobiologie de la Méditerranée Sharon Crook, Arizona State University Andrew Davison, Centre National de la Recherche Scientifique Erik De Schutter, Okinawa Institute of Science and Technology Shaul Druckmann, Janelia Research Campus/HHMI Chris Eliasmith, University of Waterloo Jeremy Freeman, Janelia Research Campus/HHMI Michael Hausser, University College London Jeanette Hellgren Kotaleski, Karolinska Institutet Fritjof Helmchen, University of Zurich David Kleinfeld, University of California, San Diego Jeff Magee, Janelia Research Campus/HHMI Robert McDougal, Yale School of Medicine Eilif Muller, École Polytechnique Fédérale de Lausanne Hanchuan Peng, Allen Institute for Brain Science Ruben Portugues, Max Planck Institute of Neurobiology Mark Schnitzer, HHMI/Stanford University Ivan Soltesz, Stanford School of Medicine Nelson Spruston, Janelia Research Campus/HHMI Misha Tsodyks, Weizmann Institute of Science Registration is free, but places are limited.*Registration closes 18th May 2016*. For more details and to apply for participation go to https://www.janelia.org/you-janelia/conferences/collaborative-development-d…. ----------------------------------------------------- Padraig Gleeson Room 321, Anatomy Building Department of Neuroscience, Physiology& Pharmacology University College London Gower Street London WC1E 6BT United Kingdom +44 207 679 3214 p.gleeson(a)ucl.ac.uk -----------------------------------------------------

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MICCAI Challenge on Neural Circuit Reconstruction
by Jan Funke May 3, 2016

May 3, 2016

Dear colleagues, We would like to draw your attention to the MICCAI challenge "CREMI: Circuit Reconstruction from Electron Microscopy Images" (http://cremi.org/) As of May 1st, the training phase of the challenge has opened. We provide three volumes with dense neuron and synapse segmentation, along with annotations for pre- and post-synaptic partners (http://cremi.org/data.html) The goal of this challenge is to evaluate algorithms for automatic reconstruction of neurons and neuronal connectivity from serial section electron microscopy data. The comparison is performed not only by evaluating the quality of neuron segmentations, but also by assessing the accuracy of detecting synapses and identifying synaptic partners. The challenge is carried out on three large and diverse datasets from adult Drosophila melanogaster brain tissue, comprising neuron segmentation ground truth and annotations for synaptic connections. A successful solution would demonstrate its efficiency and generalizability, and carry great potential to reduce the time spent on manual reconstruction of neural circuits in electron microscopy volumes. Follow us on Twitter for updates (https://twitter.com/cremi_challenge) and feel free to contact us at challenge(a)cremi.org. Regards, The CREMI organizers (Jan Funke, Stephan Saalfeld, Davi Bock, Srini Turaga, and Eric Perlman)

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