June 2018 - Comp-neuro - lists.cnsorg.org

Postdoc position in calcium imaging of Fragile X zebrafish

by Geoffrey Goodhill

Geoff Goodhill's lab at the University of Queensland is looking for an experimental postdoc to analyse a zebrafish model of Fragile X syndrome using behavioural and calcium imaging approaches. The salary range is AU$81k-87k (US$60-64k). We are particular interested in how neural coding emerges over development in these fish. The project will involve both high-speed video recording of zebrafish larvae behaviour, and large scale 2-photon recording of GCaMP6s neural activity using confocal and light-sheet microscopy. The successful candidate will work closely with an interdisciplinary team with a strong computational focus. A new review paper discussing some of the relevant background is Avitan L & Goodhill GJ (2018). Code Under Construction: Neural Coding Over Development Trends in Neurosciences, online June 20th https://www.cell.com/trends/neurosciences/abstract/S0166-2236(18)30158-9 The University of Queensland (UQ) is ranked in the top 3 universities in Australia and the top 100 in the world. The Goodhill lab is part of the Queensland Brain Institute at UQ, a leading neuroscience institute consisting of over 40 labs, including ~100 PhD students and ~100 postdocs. For more details and to apply please see the following link: http://jobs.uq.edu.au/caw/en/job/504708/postdoctoral-research-fellow The closing date is July 25th AEST. Informal enquiries are also welcome. Professor Geoffrey J Goodhill Queensland Brain Institute and School of Mathematics & Physics University of Queensland St Lucia, QLD 4072, Australia Email: g.goodhill(a)uq.edu.au<mailto:g.goodhill@uq.edu.au> http://www.qbi.uq.edu.au/professor-geoffrey-goodhill

June 30, 2018

PhD and post-doctoral positions in Electrophysiology / Brain-machine interface at the Université de Sherbrooke, Canada

by Jean Rouat

Dear list, We have PhD and one post-doctoral positions in our research group. Please communicate with my colleague Eric Plourde for further details. 1) PhD positions in Electrophysiology / Brain-machine interface at the Université de Sherbrooke, Canada (co-supervision at the University of Minnesota, USA) for IC implants Auditory implants aim at restoring audition by stimulating a specific structure of the auditory system with an electrode array. The most successful auditory implant, the cochlear implant that stimulates the spiral ganglions in the cochlea, has allowed more than 325 000 people worldwide to regain audition. However, cochlear implants are not appropriate for patients that have a disfunctionnal auditory nerve or for which the cochlea cannot be implanted. Alternative implants have therefore been developed such as the auditory midbrain implant (AMI) that stimulates a structure named the inferior colliculus (IC). One aspect that limits the development of the AMI is the lack of knowledge regarding the optimal approach to stimulate the IC. The proposed project aims at gaining more insight into the optimal design of stimulation patterns for the IC. Objectives: Design optimal inferior colliculus stimulation patterns using adaptive filters specifically adapted for neural signals: the neural activity will be recorded in the auditory cortex and optimal stimulation in the inferior colliculus will be evaluated using a closed-loop approach. A financial support will be provided. Requirements: - Excellent academic record. - Master’s degree in biomedical engineering, electrical engineering, computer engineering, physics, biophysics or other related field with a strong background in mathematics and signal processing. - Willing to conduct experiments in electrophysiology to record the neural activity of the auditory system. No prior knowledge in electrophysiology is required. - Excellent ability to communicate in English, knowledge of French is considered an advantage. Interested candidates should send their CV, academic transcripts and relevant publications as well as the names of 2 references to Prof. Eric Plourde. Contact: Eric Plourde, Eng., Ph.D., Université de Sherbrooke (eric.plourde(a)usherbrooke.ca) 2) Postdoctoral position in statistical signal processing / Brain-machine interface at the Université de Sherbrooke A retinal prosthesis aims at giving back vision to blind people. To do so, an external camera captures visual scenes and sends this information to an electrode array, which is positioned in the eye, in order to stimulate directly the retina. The electric pulses from the electrodes are sent to the brain along the optic nerve and interpreted as sight. The objective of this study is to decode a perceived image using Bayesian decoding approaches. Many types of patterns can be used to stimulate the different electrodes comprising the array and not all are efficient. The research proposal aims at simulating a perceived image using an adapted stimulation approach and Bayesian decoding and comparing it with an image obtained with traditional stimulation approaches. The contract is for a 6-months period. Requirements: - Ph.D. degree in statistical signal processing, biomedical engineering, bio-informatics or other related field - Proven publication record - Excellent ability to communicate in English. Interested candidates should send their CV, academic transcripts and relevant publications as well as the names of 2 references to Prof. Eric Plourde. Contact: Eric Plourde, Eng., Ph.D., Université de Sherbrooke (eric.plourde(a)usherbrooke.ca) ==================================================== The Université de Sherbrooke is a French-speaking institution located in the province of Quebec, Canada, and the heart of an international research pole. It is host to more than 40 000 students from over 120 different countries worldwide. (Source: UdeS) ==================================================== Jean Rouat, Prof., coord. IGLU, http://iglu-chistera.github.io Université de Sherbrooke Université de Montréal Member of the centre for Interdisciplinary research Professeur titulaire, Professeur associé in Music Media and Technology NECOTIS: Computational Neurosciences Vision, neuroscience Lab McGill Schulich School of Music and Intelligent Signal Processing FAS- Sciences biologiques 527 Sherbrooke St. West Faculté de génie, GEGI, C1-3108 90 avenue Vincent-d’Indy Montreal, Qc, 2500 boul. de l'université Montréal, Qc, Canada, H3A 1E3 Sherbrooke, Québec Canada, H3C 3J7 Canada, J1K 2R1 Tél.: +1(819)-821-8000 ext. 63864 http://www.gel.usherbrooke.ca/rouat http://www.gel.usherbrooke.ca/necotis http://www.usherbrooke.ca/gelecinfo/fr/pers/profs/rouj-fr/ Jean.Rouat(a)umontreal.ca ou Jean.Rouat(a)usherbrooke.ca Publications: https://www.gel.usherbrooke.ca/rouat/publications/publiDeJRouat.html

June 29, 2018

PhD opening in Machine learning for Neural Encoding of Naturalistic Auditory Scenes

by Nicolas Farrugia

Dear list, We invite applications for a fully-funded PhD between Université de Montréal, computer science department, and IMT Atlantique, Brest, France. The goal is to model the perception of complex natural auditory stimuli using signals on dynamic brain graphs, and deep learning. Details are here : https://t.co/963vd9Pizg and below Deadline for application is July 15th. The project aims to model natural auditory perception using artificial neural networks and graph signal processing, applied to human functional magnetic resonance imaging (fMRI) and electroencephalograph (EEG) data. Recent advances in artificial intelligence are largely due to the outstanding performance obtained by deep neural networks on the classification of composite natural stimuli. Deep learning however still faces important challenges with natural auditory perception [1], in particular in complex, noisy scenes involving several simultaneous sources. This thesis will use human neuroimaging data to improve the ability of artificial networks to classify natural auditory stimuli. Recent works have demonstrated the feasibility of building artificial models to link computational musical features with brain activity [2]. Such models perform as well as human listeners on both music, and simple speech discrimination tasks [3]. The internal layers of the deep networks have also been used to predict brain activity related to natural sounds, by modeling each individual voxel of fMRI activity using combinations of feature maps [3]. We propose to investigate extensions of the current approaches to consider graph convolutional networks [4], signal processing on graphs [5], and to model temporal signals on dynamic graphs [6]. We will build a series of artificial models, using extensive recordings of EEG/fMRI brain activity acquired from participants performing auditory tasks of increasing complexity. This PhD project is a collaboration between the laboratories of Dr. Nicolas Farrugia and Dr Vincent Gripon (Brain Inspired Artificial Intelligence Project, at IMT Atlantique, Brest, France), and the lab of Dr. Pierre Bellec (NeuroMod - Courtois Project on Neuronal Modelling - CRIUGM, Department of Computer Science and Operational Research, Université de Montréal, Montréal, Qc, Canada). The candidate will be expected to share their time between Montreal and Brest. IMT Atlantique is a public technological university focusing on the training of engineers at the MSc. level and junior researchers at the PhD level. Université de Montréal is a world-renowned institution, training elite scientist, and is currently one of the main hubs for artificial intelligence and neuroinformatics research in North America.

June 29, 2018

The Journal of Mathematical Neuroscience - recent articles

by Stephen Coombes

The Journal of Mathematical Neuroscience publishes research articles on the mathematical modeling and analysis of all areas of neuroscience. The new Impact Factor of the journal is 2.414 The current list of journal articles is available at http://www.mathematical-neuroscience.com/ : Investigating the Correlation–Firing Rate Relationship in Heterogeneous Recurrent Networks Andrea K. Barreiro and Cheng Ly https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Effect of Neuromodulation of Short-term Plasticity on Information Processing in Hippocampal Interneuron Synapses Elham Bayat Mokhtari, J. Josh Lawrence and Emily F. Stone https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Analysis of an Attractor Neural Network’s Response to Conflicting External Inputs Kathryn Hedrick and Kechen Zhang https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Saddle Slow Manifolds and Canard Orbits in R^4 and Application to the Full Hodgkin–Huxley Model Cris R. Hasan, Bernd Krauskopf and Hinke M. Osinga https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Kernel Reconstruction for Delayed Neural Field Equations Jehan Alswaihli, Roland Potthast, Ingo Bojak, Douglas Saddy and Axel Hutt https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… All articles are Open Access. ------------------------------------------------------- Stephen Coombes Professor of Applied Mathematics School of Mathematical Sciences Nottingham, UK Tel: 0115 846 7836 http://www.maths.nott.ac.uk/~sc/ ------------------------------------------------------- This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

June 28, 2018

Postdoc position in Computational Neuroscience - CRM Barcelona

by Klaus Wimmer

A fully funded POSTDOC POSITION in computational neuroscience is available in the lab of Klaus Wimmer, Computational Neuroscience Group at the CRM, Barcelona, Spain. *Profile* We are looking for an enthusiastic and scientifically curious researcher with a strong interest in computational neuroscience. The perfect candidate has a strong mathematical, physical or engineering background, scientific programming skills (Matlab, Python), and a keen interest in biological neural systems. Knowledge in computational neuroscience, dynamical systems, machine learning or advanced statistics is a plus. Good team spirit is a must. *Research topic* The neural basis of decision making and working memory has been studied extensively, yet our understanding of how distributed circuits in the brain perform these cognitive functions is only at the beginning. Models of cortical circuits can shed light on the underlying neural network dynamics. The Postdoc will work on building such models and on cutting-edge analysis of large-scale neural activity recordings (neuronal population recordings, fMRI, EEG). *The lab* The Computational Neuroscience Group is based at the Centre de Recerca Matemàtica at the campus of the Universitat Autònoma de Barcelona. It is a joint effort of Alex Roxin and Klaus Wimmer, and forms part of a larger network of theoretical and systems neuroscience labs in Barcelona. The successful candidate will benefit from a vibrant and stimulating research community and will have the opportunity of enjoying a lively city. More information can be found at: https://sites.google.com/view/wimmerlab *How to apply* Interested candidates should e-mail their application as a single pdf file to Klaus Wimmer, kwimmer(a)crm.cat, with the subject “Postdoc 2018”. The application should include: (1) CV with publication list, (2) a brief description of research experience and interests, (3) contact information for two references. The position is available immediately and applications will be accepted until it is filled. Informal inquiries are welcome. -- Klaus Wimmer Ramón y Cajal researcher at Centre de Recerca Matemàtica Campus de Bellaterra, Edifici C 08193 Bellaterra (Barcelona) Spain Tel. +34 935 86 85 15 https://sites.google.com/view/wimmerlab

June 27, 2018

fully funded PhD position in computational neuroscience with Prof. Laurenz Wiskott in Bochum, Germany

by Laurenz Wiskott

Please forward this job advertisement to candidates who might be interested. Thanks, Laurenz Wiskott. ___________________________________________________________________________ Open position for a PhD student with Prof. Laurenz Wiskott at the Institute for Neural Computation, Bochum, Germany ___________________________________________________________________________ Institute: Institute for Neural Computation Ruhr-University Bochum Universitaetsstr. 150 D-44801 Bochum, Germany, EU The Institute for Neural Computation is a central research institute at the Ruhr-University Bochum, see https://www.ini.rub.de/. It focuses on the dynamics and learning of perception and behavior on a functional level but is otherwise very diverse, ranging from neurophysiology and psychophysics over computational neuroscience to machine learning and technical applications. Research group: Prof. Dr. Laurenz Wiskott, see http://www.ini.ruhr-uni-bochum.de/PEOPLE/wiskott/ Research topics: We are looking for an outstanding candidate who will be working on a model of the hippocampus and neocortex investigating the interplay between episodic memory and semantic memory. We use methods from neural networks and machine learning. It is also planned to simulate experiments done with humans by our experimental partners in Bochum and Münster. The position is part of a team working jointly on developing a system-level model of hippocampal function for memory and navigation. This is being doing in close interaction with a team working on similar questions from the machine learning perspective. Teaching: There is a teaching load of 3 hours per week during the semester, in particular for a programming course in python. Time: The appointment will be for three years and can then be extended for one more year if needed. Requirements: Candidates should have an education (equivalent to a MSc) in computer science, physics, mathematics, electrical engineering or any related field. Required are strong mathematical and programming skills (ideally in python) as well as the ability to communicate and work well in a team. Salary: Salary is 75% of salary scale TV-L E13. Inquiries: Informal inquiries can be addressed to Prof. Laurenz Wiskott <laurenz.wiskott(a)rub.de>. Application: Applications (CV, transcript of records for MSc and BSc, statement of purpose) should be sent as a single file pdf to Prof. Laurenz Wiskott <laurenz.wiskott(a)rub.de>. Ruhr-University Bochum is committed to equal opportunity in employment and gender equality in its working environment. We therefore look forward to applications from qualified women. Applications from appropriately qualified handicapped persons are also encouraged.

June 27, 2018

2018 NEURON Summer Course reminder

by Ted Carnevale

If you are interested in this year's NEURON Summer Course but haven't signed up yet, you should act quickly because only a few seats remain available, and the registration deadline is July 16. The course runs from Monday, August 6, through Saturday, August 11, and will be held at Emory University in Atlanta, Georgia. It will present a thorough introduction to computational modeling of neurons and networks with NEURON, and is suitable for individuals at all levels of expertise. For more information and the on-line registration form, see http://www.neuron.yale.edu/neuron/static/courses/summer2018/summer2018.html --Ted

June 26, 2018

Save your space today: FENS Satellite Symposium "From Scanner to Bedside"

by Markus Butz Ostendorf

Dear colleagues, My apologies for cross postings. There are a few spaces left on the FENS Satellite Symposium "From Scanner to Bedside - What connectome and gene expression say about brain diseases" on 6 July in the beautiful guest house "Harnack House" of the Max-Planck Society in Berlin-Dahlem. Save your space today by registration via the symposium's website: https://www.biomax.com/symposiums/from-scanner-to-bedside/ Free registration, lunch and refreshments provided! Looking forward to seeing you in Berlin Markus -- Dr. rer. nat. Markus Butz-Ostendorf Product Manager Biomax Informatics AG Robert-Koch-Str. 2, 82152 Planegg, Germany Registergericht: Amtsgericht München, HRB 134442 Vorstand: Dr. Klaus Heumann Vorsitzender des Aufsichtsrates: Prof. Dr. Hans-Werner Mewes Tel: +49 89 895574-862 Fax: +49 89 895574-825 Email: markus.butz-ostendorf(a)biomax.com Website: http://www.biomax.com PGP: https://ssl.biomax.de/pgp/

June 26, 2018

PostDoc available in Neuromorphic Computing within the Human Brain Project

by Thomas Nowotny

Dear all, Within sub-project 9 of the Human Brain Project (HBP) we are looking for a PostDoc to work on applications of neuromorphic computing. You will join a dynamic team of researchers in computational Neuroscience and biomimetic robotic control at the University of Sussex and work on cutting edge prototype neuromorphic systems developed at Heidelberg (BrainScaleS, https://electronicvisions.github.io/hbp-sp9-guidebook/pm/pm.html) and Manchester (SpiNNaker, https://electronicvisions.github.io/hbp-sp9-guidebook/mc/mc_index.html) Excellent programming skills and a keen interest in applying neuromorphic computing to interesting problems will be essential. Previous experience with neuromorphic computing and/or machine learning will be a big plus. Deadline: 24 July 2018 Duration: currently funded until end of March 2020; possible extension into the next funding phase of the HBP. Details & apply: http://www.sussex.ac.uk/about/jobs/research-fellow-in-neuromorphic-computin… Queries: Prof Thomas Nowotny (t.nowotny(a)sussex.ac.uk<mailto:t.nowotny@sussex.ac.uk>) With kind regards, Thomas Nowotny -- Prof Thomas Nowotny Director of Research and Knowledge Exchange School of Engineering and Informatics University of Sussex Falmer, Brighton BN1 9QJ, UK Phone: +441273678593 FAX: +441273877873

June 25, 2018

Neuronal morphology and structure workshop at CNS - 2018

by André Castro

Dear all, We are pleased to announce the 4th edition of the Neuronal morphology and structure workshop at [CNS*2018](https://www.cnsorg.org/cns-2018), Seattle, USA. The workshop will be held at the Allen Institute for Brain Science, July 17 . Our confirmed invited speakers are the following: - Hollis Cline (Scripps Research Institute) (keynote) -- "In vivo time-lapse imaging analysis of neuronal structure and functional plasticity" - Ruth Benavides-Piccione (Instituto Cajal, Spain) -- "The microanatomy of pyramidal cells" - Staci Sorensen[,](http://www.treestoolbox.org/CNS2018_dendrites_workshop/speakers… (Allen Institute, USA) -- "Morphological, electrophysiological and transcriptional descriptions of cortical cell types" - Erik De Schutter (OIST, Japan) -- "The Purkinje cell dendrite causes its unique firing rate-dependent phase response curve" - Uygar Sümbül (Allen Institute, USA) -- "Quantifying neuroanatomy" - Lida Kanari (EPFL, Switzerland) -- "Randomness and structure in artificially generated neuronal networks" - Casey Schneider-Mizell (Janelia Research Campus, USA) -- "The neuroanatomy of connectivity in the Drosophila larva" - Kurt Haas (University of British Columbia, Canada) -- "Dynamic morphometrics: Rapid time-lapse imaging and quantification of experience-driven dendrite growth" - Sophie Laturnus (Universität Tübingen, Germany) -- "A systematic comparison of neural morphology representations for cell type discrimination" - Hongkui Zeng (Allen Institute, USA) -- ''Morphology as a key feature for neuronal cell type classification'' Please see our [website](http://www.treestoolbox.org/CNS2018_dendrites_workshop/index.html) for more details. Organising Committee: Alexander Bird (Ernst Strüngmann Institute and FIAS, Frankfurt) André Castro (Ernst Strüngmann Institute and FIAS, Frankfurt) Hermann Cuntz (Ernst Strüngmann Institute and FIAS, Frankfurt)

June 20, 2018