- Comp-neuro - lists.cnsorg.org

Call for community review: 2 new neuroscience SBPs

by INCF

Two calls for community review: 1. Digital SWC Reconstructions Describing Neuron Morphology (SWC) 2. SPARC Data Structure Feedback from the community is an important part of our review process; it helps us ensure that the standard has community support and is useful and practical to the community. By commenting, you contribute to improving the standard for current and future users! 1. Digital SWC Reconstructions Describing Neuron Morphology (SWC) SWC files (file extension of .swc) are text-based (ASCII text) files that describe three-dimensional neuronal or glial morphology. These digital reconstructions represent morphology as a vectorized tree structure, made of a series of connected nodes. An SWC file contains a series of text-based rows where each neuron node is described by a single row of only seven space-separated values. The format is simple and intuitive; a parser of or writer to the format could be implemented by anyone with knowledge of any programming language. With an open archive and freely available structure editor, the SWC system facilitates community-wide pooling of data for building biophysically realistic neuronal models and studying the morphological variation between neurons, contributing to a greater neuroscientific cooperation and openness. Review by Aug 15 Learn more: incf.org/commentaries/swc <https://www.incf.org/commentaries/swc> 2. SPARC Data Structure Financially backed by the NIH Common Fund, SPARC is a large-scale project which aims to deepen our knowledge of nerve-organ interactions. With an initial focus on bioelectronic medicine, the SPARC consortium created the SPARC data structure (SDS), a file and metadata organizational scheme inspired by the Brain Imaging Data Structure (BIDS). This data structure has proven capable of handling complex datasets from multiple and heterogeneous species, measurement techniques, and spatial scales. One of the primary purposes of SDS is to increase the integrity of scientific research by promoting FAIR and open science practices, particularly by facilitating the generation of well-annotated, organized, standardized, and shared biomedical datasets. Review by Aug 15 Learn more: incf.org/commentaries/sparc <https://www.incf.org/commentaries/sparc> Thanks for your help! /The INCF Team

June 26, 2023

Computational Neuroscience Postdoc position in New York

by Salvador Dura-Bernal

A Postdoc position is now available in the Dura-Bernal Lab<http://dura-bernal.org/> at the State University of New York (SUNY) Downstate Health Sciences University (Brooklyn, New York), working on a new exciting multidisciplinary project entitled "Restoring motor function after spinal cord injury using multiscale modeling to decode neural latent dynamics from motor cortex EEG." The position is funded by New York State (NYS) Department of Health (DOH) Spinal Cord Injury Research program. The project aims to improve brain-machine interface decoders by combining multiscale modeling of motor cortex circuits, analysis of low-dimensional neural manifolds associated with behavior, and realistic simulation of EEG signals. See our recent Cell Reports publication describing the multiscale motor cortex model and behavior-related neural manifolds: www.cell.com/cell-reports/fulltext/S2211-1247(23)00585-5<http://dura-bernal.org/www.cell.com/cell-reports/fulltext/S2211-1247(23)005…> For more details and how to apply visit: http://dura-bernal.org/postdoc-2023<https://t.co/aGDh79EjyE> (Please share!) ________________________________ The contents of this email message and any attachments are confidential and are intended solely for the addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify sender by reply email or by (718) 270-HELP.

June 25, 2023

Registration for the Bernstein Conference 2023 in Berlin is open now

by Alexander Lammers

***Registration for the Bernstein Conference 2023 in Berlin is open now*** ___ The Bernstein Conference Each year the Bernstein Network invites the international computational neuroscience community to the annual Bernstein Conference for intensive scientific exchange. It has established itself as one of the most renowned conferences worldwide in this field, attracting students, postdocs, and PIs from around the world to meet and discuss new scientific discoveries. www.bernstein-conference.de<http://www.bernstein-conference.de> ___ Important Dates * Bernstein Conference: September 26 - 29, 2023 * Abstract submission for posters: July 19, 2023, 15:00 CEST * Travel grant applications: July 19, 2023 * Early registration: July 19, 2023 ___ Registration Registration for the Bernstein Conference is open now. Register until July 19, 2023, and profit from reduced conference fees. All information: https://bernstein-network.de/bernstein-conference/registration/ ___ Abstract Submission We invite the computational neuroscience community to submit their abstracts. The abstract submission for posters is open until July 19, 2023, 15:00 CEST. All accepted abstracts will be published online and will be citable via Digital Object Identifiers (DOI). Abstract submission: https://bernstein-network.de/bernstein-conference/abstract-submission/ ___ Travel Grants Students, PhD candidates, and postdocs can apply for travel grants. Travel grant application: https://bernstein-network.de/bernstein-conference/early-career-scientists/t… ___ Invited Speaker Keynote Marlene Cohen (University of Chicago, USA) Invited Talks Tiago Branco (Sainsbury Wellcome Center, UK) Stefano Fusi (Columbia University, USA) Ann Kennedy (Northwestern University, USA) Julija Krupic (University of Cambridge, UK) Wiktor Mlynarski (LMU Munich, Germany / Institute of Science and Technology, Austria) Adrien Peyrache (McGill University, Canada) Kanaka Rajan (Icahn School of Medicine at Mount Sinai, USA) Christopher Summerfield (University of Oxford and Deepmind, UK) Julia Veit (Albert-Ludwigs-Univesität Freiburg, Germany) ___ Conference Committee Robert Gütig (Conference Chair) Tatjana Tchumatchenko (Program Chair) Srdjan Ostojic (Program Vice Chair) Anna Levina (Workshop Chair) Maria Eckstein (Workshop Vice Chair) & Athena Akrami, Ann Hermundstad, Mehrdad Jazayeri, Christian Leibold, Ashok Litwin-Kumar, Ida Momennejad, Nicole Rust, Andrew Saxe, Daniela Vallentin, Friedemann Zenke. ___ Contact For any further questions, please contact: bernstein.conference(a)fz-juelich.de<mailto:bernstein.conference@fz-juelich.de> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

June 23, 2023

1 PhD position on: New methods for realistic and comfortable experiences in AR

by Agostino Gibaldi

We are inviting applications for one fully funded PhD position (3 years) in the Department of Informatics, Bioengineering, Robotics, and Systems Engineering <https://dibris.unige.it/en>, at the University of Genoa (IT), in collaboration with Magic Leap <https://www.magicleap.com/en-us/>. The research theme focuses on realistic and comfortable experiences in Augmented Reality (more info in the attached call for position). Interested applicants are welcome to reach out for more information about the theme and the position. The official call can be found here: https://unige.it/dottorati-di-ricerca You can apply from June 09 at 03.00 pm (italian time) to July 10 at 12.00 noon (italian time) at this page: https://unige.it/en/students/phd-programmes Best, Agostino Gibaldi, PhD Human Vision Scientist Magic Leap *New methods for realistic and comfortable* *experiences in AR – University of Genoa* *Curriculum: *Industry 4.0 *Hosting Institution: *University of Genoa *Department: *Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS) *Tutors:* Silvio P. Sabatini, Andrea Canessa, Gerrit Maus, Agostino Gibaldi *Description:* Optical see-through (OST) augmented reality head-mounted displays (HMD) have emerged as a key asset in several application fields. In OST HMDs the direct view of the world is mostly preserved and there is no perspective conversion in viewpoint and field of view, as with video see-through (VST) systems. This aspect confers a clear advantage over VST solutions, particularly when used to interact with close objects. Although there have been significant improvements to performance and comfort of OST HMDs, limitations associated with human perception still remain to be addressed. In order to provide the user with a realistic, natural and comfortable visual experience, a thorough and accurate knowledge of eye characteristics and HMD geometry must be assumed. These quantities are usually calibrated on a per-device and per-user basis, or modeled from scientific literature. A deviation of the actual values from the expected ones can result in incorrect camera placement, spatial distortions and non-uniformities, thus triggering discomfort in VR/AR. The goal of this research project is to develop methods and techniques to assess and mitigate discomfort and perceptual inconsistencies between real and augmented visual content in OST HMDs. A joint experimental and modeling approach will be followed in order to: 1. investigate methods to evaluate different sources of discomfort/mismatch; 2. develop subjective and objective methods to quantify the originated discomfort; 3. investigate strategies to mitigate the sources of discomfort/mismatch in AR/VR devices. *Requirements:* Applicants are expected to: 1) have a keen interest in Vision Science and in Augmented Reality, 2) have good programming skills in at least one language (Matlab, C/C++, Python, C#), 3) work well in group problem solving situations, 4) have intermediate communication skills (oral and written) in English or better. Experience in Unity 3D is a plus. *References:* [1] Konrad, R., Angelopoulos, A., & Wetzstein, G. (2020). Gaze-contingent ocular parallax rendering for virtual reality. ACM Transactions on Graphics (TOG), 39(2), 1-12 [2] Lambooij, M. T., IJsselsteijn, W. A., & Heynderickx, I. (2007). Visual discomfort in stereoscopic displays: a review. Stereoscopic Displays and Virtual Reality Systems XIV, 6490, 183-195. [3] Gibaldi A., Liu Y., Kaspiris-Rousellis C., Mahadevan M., Vlaskamp B.NS, Maus G.W. Vertical vergence and screen alignment with see-through head-mounted displays. ECVP 2023. *Company name and link (for industrial projects):* Magic Leap Inc. (www.magicleap.com) *Number of positions available: 1* *Main Research Sites* *1.* DIBRIS, via Opera Pia 13, 16145 Genoa, Italy, *2.* Macic Leap Inc., Andreasstrasse 5, 8050 Zürich, Switzerland *Contacts:* Email: silvio.sabatini(a)unige.it, gmaus(a)magicleap.com *Funding Scheme:* This doctorate grant is co-funded by PNRR program DM-117

June 22, 2023

Endowed Professorship "Machine Learning for Clinical Neuroscience"

by Philipp Berens

Dear all, we are currently advertising an Endowed professorship "Machine Learning for Clinical Neuroscience" (https://www.academics.com/jobs/w3-stiftungsprofessur-fuer-maschinelles-lern…) at the University of Tübingen. We are looking for candidates that perform innovative research on the application and development of new machine learning methods in clinical neuroscience, in particular for early detection and prediction of disease progression. This can include work on topics such as explainability, safety and robustness of machine learning methods in clinical settings. It would be great if candidates had worked with multimodal data with clinical relevance (e. g. MRI, fMRI, EEG, electrophysiology, omics data, data from sensors of wearables) as well as cohort data (UKBiobank, NAKO, etc.). Tübingen offers a first-rate environment at the intersection of neuroscience and AI/ML research with the Excellence Cluster for Machine Learning in Science, the Tübingen AI Center, the Max Planck Institutes for Intelligent Systems and Biological Cybernetics, the Hertie Institute for Clinical Brain Research and many other institutions! We are looking forward to your application by July 20th. Best Philipp -- Professor of Data Science, Director Hertie Institute for AI in Brain Health Medical Faculty of the University of Tübingen www.berenslab.org

June 22, 2023

[job post] Open PhD positions on neuromorphic perception and control for soft robots

by Chiara Bartolozzi

We are looking for three PhD fellows interested in developing neuromorphic systems for robots. They will team up to look at the different aspects involved in developing neuromorphic circuits and computation for sensing, perception, and actuation for soft biomimetic robots. We will aim at coupling soft materials, sensory transduction, neuromorphic circuits and computation, and soft actuation, towards the design of robots that can seamlessly and gently interact with their environment. Each PhD will have their own multi-disciplinary research goals and will be co-supervised by leading scientists in the complementary disciplines: Neuromorphic distributed intelligence for soft robots – Computation with spiking neural networks for haptic perception and closed loop control of soft robots – Supervisors: C. Bartolozzi<https://edpr.iit.it/> & B. Mazzolai<https://bsr.iit.it/> Neuromorphic distributed intelligence for soft robots – Design of neuromorphic circuits on flexible substrates for sensing and computation – Supervisors: C. Bartolozzi<https://edpr.iit.it/> & L. Beccai<https://sbrp.iit.it/> Online neuromorphic perception and actuation for robots – Italian Institute of Technology – Supervisors: C. Bartolozzi<https://edpr.iit.it/>, S. Soldado-Magraner<https://bri.ucla.edu/people/saray-soldado-magraner/> & E. Donati<https://services.ini.uzh.ch/people/elisa> Location: Italian Institute of Technology, via San Quirico 19D, Genova, Italy https://iit.it Enrolment: DRIM PhD School @ University of Genova https://drim.i-rim.it/en/ Official call (with guidelines for applications): https://unige.it/en/students/phd-programmes PhD themes description: https://drim.i-rim.it/wp-content/uploads/2023/05/Research-Themes-Hostile-an… - checkout Themes 3,4<https://drim.i-rim.it/wp-content/uploads/2023/05/Research-Themes-Hostile-an…>,5 Deadline for application: June 30th

June 22, 2023

CFP - IROS 2023 Workshop on World Models and Predictive Coding in Cognitive Robotics

by nagai.yukie＠mail.u-tokyo.ac.jp

Dear colleagues, **************************** Call for Posters and Participation Workshop on World Models and Predictive Coding in Cognitive Robotics 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2023) **************************** We are inviting contributions to our IROS 2023 workshop. We would like to invite workshop attendees to submit an extended abstract explaining their current work related to world models and predictive coding in cognitive robotics. [ Website ] https://world-model.emergent-symbol.systems/ Contact email: taniguchi(a)em.ci.ritsumei.ac.jp (Tadahiro Taniguchi, Ritsumeikan University) [ Important Dates ] Paper submission deadline: 5th August 2023 Notification of acceptance: 19th August 2023 Camera-ready submission: 10th September 2023 Workshop day: 5th October 2023 [ Call for Contributions ] We encourage researchers to submit 1-2 page extended abstracts or a preprint of relevant work. There is no page limitation for the preprint. Accepted abstracts will be posted on the workshop website and will not appear in the official IEEE proceedings. The reviewing process is single-blind and will be carried out by the workshop organizers. Please submit your extended abstract via the Google form: https://forms.gle/Sw7UtX1ihtq4vpgA9 (The URL is also provided on the website) Accepted papers will have the opportunity to present their work/ideas in a poster session. Additionally, a few select submissions will have the chance to give a short talk, while others will give a flash talk. [ Special Issue ] Furthermore, a selected number of papers from the poster sessions will be invited to submit their novel work to the Special Issue proposed in the journal "Advanced Robotics.” [ Awards ] The Best Cognitive Robotics Paper Award, supported by the Technical Committee of Cognitive Robotics, will be awarded to the best paper. The recipient of the award will receive a prize of $300. [ Objectives ] This workshop will explore new frontiers in robotics, focusing on world models, predictive coding, probabilistic generative models, and the free energy principle. The ultimate goal of cognitive and developmental robotics is to create autonomous robots capable of actively exploring their environment, acquiring knowledge, and continuously learning skills. Crucially, to develop robots that learn through interactions with their environment, their learning processes should emulate human cognitive development and learning, which are based on engagement with the physical and social world. This workshop specifically focuses on world models and predictive coding in cognitive robotics. World models have recently garnered significant interest in artificial intelligence, as cognitive systems utilize these models to improve future sensory predictions and optimize their policies or controllers. In neuroscience, predictive coding posits that the brain constantly anticipates its inputs and adjusts its models to manage dynamics and control behavior in its environment. Both concepts may underlie the cognitive development of robots and humans capable of continuous or lifelong learning. The workshop aims to provide a platform for researchers and practitioners in cognitive robotics to exchange ideas and explore new avenues for the development of autonomous cognitive and developmental robots. This enriching experience will contribute to the growth and advancement of the field of cognitive robotics. [ Invited Speakers ] (planned) Tetsuya Ogata (Waseda University, Japan) Pablo Lanillos (Donders Institute for Brain, Cognition, and Behaviour, Netherlands) Giulio Sandini (Italian Institute of Technology, Italy) Takamitsu Matsubara (NAIST, Japan) Beren Millidge (Conjecture, UK) Danijar Hafner (UC Berkeley, United States) [ Organizers ] Tadahiro Taniguchi, Ritsumeikan University Emre Ugur, Bogazici University Masahiro Suzuki, The University of Tokyo Dimitri Ognibene, Università degli Studi di Milano-Bicocca Lorenzo Jamone, Queen Mary University of London Yukie Nagai, The University of Tokyo Tatsuya Matsushima, The University of Tokyo Tetsunari Inamura, Tamagawa University Best regards, Yukie, on behalf of the organizers — Yukie Nagai, Ph.D. Project Professor, The University of Tokyo nagai.yukie(a)mail.u-tokyo.ac.jp | https://developmental-robotics.jp CREST Cognitive Feelings: https://cognitive-feeling.jp CREST Cognitive Mirroring: https://cognitive-mirroring.org

June 21, 2023

Spanish Return of Talent Programme

by Serafim Rodrigues

Dear All, Please find below a brief summary of the *“Return of Talent Programme”* launched by the FUNDACIÓN RAMÓN ARECES. The deadline for submission of applications is* 15th October 2023.* v *OVERVIEW OF THE CALL* The aim of this call is to promote an innovative programme for the return of scientists already established abroad, so that they can develop a *relevant* *research project (in any scientific area) for a period of five years in a Spanish public research institution*. v *FUNDING CONDITIONS & DURATION* *DURATION:* *5 years* (the initial duration is 1 year, extendable annually for 4 successive additional years after a favorable evaluation by the Foundation's Scientific Council). *Note:** It must start, at the latest, 12 months after the Call results are published.* *FUNDING:* *1 grant** for the amount of 1.250.000 €* - *1st year:* 40 %. - *2nd and 3rd year:* 20% each year. - *4th and 5th year:* 10% each year. v *ELIGIBILITY & REQUIREMENTS* - *Applicant researchers:* ü *Spanish nationality*. ü *Have been residing and working on scientific projects outside Spain for a period of no less than 5 years* at the time of application. *Note:** time spent abroad (“estancias puntuales en el extranjero”) will not be considered as a period of residence, nor will the provision of services as a volunteer or any other form that does not involve financial remuneration.* ü *To have led or lead a scientific project as PI*. ü *Have a proposal from a Spanish public hospital or research center to carry out a research project.* ü Submit, together with the host institution, a significant research project, with its corresponding objectives, chronology and assessment indicators. ü Submit a declaration of intention to continue the professional activity in Spain at the end of the Programme (provided that the minimum conditions for this are met), in a joint declaration with the host institution. - *Host institutions:* ü *Spanish public hospitals or research centres. IMPORTANT NOTE: Please check the eligibility of your institution before applying.* ü Submit, together with the candidate, a five-year research project at the Spanish center with defined objectives, an established chronology and clear indicators for assessing its progress. ü Specify the contributions that the receiving center will make to support the candidate's project (human and material resources). ü To identify which facilities and laboratory will be specifically dedicated to the Programme (with the name). v *FURTHER INFORMATION* - Results to be published *before the end of 2023*. - Please access the following link for further information on the call: https://www.fundacionareces.es/fundacionareces/es/programa-de-retonorno-del… - Applications must be sent online: https://www.fundacionareces.es/areaprivada/areaprivada/index.html#/login If you are interested, please get in touch with us as we are seeking talent in the area of Mathematical, Computational and Experimental Neuroscience. Sincerely Serafim -- Serafim Rodrigues Ikerbasque Research Professor Mathematical, Computational and Experimental Neuroscience (MCEN) Group Leader *BCAM - *Basque Center for Applied Mathematics Alameda de Mazarredo, 14 E-48009 Bilbao, Basque Country - Spain Tel. +34 946 567 842 srodrigues(a)bcamath.org | www.bcamath.org/srodrigues | www.ikerbasque.net/serafim-rodrigues Old Mathematicians never die They just "tend to infinity" -Anonymous *(**matematika mugaz bestalde)*

June 21, 2023

Postdoctoral position Lyon

by DI VOLO MATTEO

A post-doctoral position is open in computational neurosciences at the Neurobiology of Executive Function lab at the Stem Brain Research Institute in Lyon (https://www.sbri.fr/).The research project aims to understand the neural mechanisms of learning during decision making. The project includes the development of a biophysical model of neuronal networks and neural mass models [1] for decision making and adaptive behaviour. The model will be developed in synergy with data analyses of monkeys electrophysiology data during task performances [2]. The successful candidate will be part of a team with experts in computational/theoretical neurosciences and will benefit from the availability of state of the art recordings at SBRI [2] and, more in general, of the rich neuroscience environment in Lyon. We welcome applicants with diverse scientific backgrounds, including, neuroscience, mathematics, physics, and engineering. We are especially interested in applicants with good programming skills (e.g. Python, C++). If interested, please take contact with Matteo di Volo: matteo.divolo(a)univ.lyon1.fr<mailto:matteo.divolo@univ.lyon1.fr> -- Matteo di Volo Junior Professor Lyon 1 University Stem and Brain Research Institute INSERM https://sbri.fr/public-profile/124/single-member/

June 21, 2023

New PhD position at Charité Berlin

by Roshan Rane

Dear Comp-neuro group, we offer a PhD / PostDoc position (4 years, 100%) at Charité - Universitätsmedizin (Berlin, Germany) in “Machine / Deep Learning in Neuroimaging for Psychiatric Research” in the framework of the TRR 265 "Losing and regaining control over drug intake". Please see the job advertisement below and forward to potential candidates. The advertisement is posted at: https://www.linkedin.com/jobs/view/3625491271/ ____________________________________________________ Job opening: PhD / PostDoc Position (100%, 4 years) “Machine / Deep Learning in Neuroimaging for Psychiatric Research” We are seeking a highly motivated and talented individual to join our research team as a PhD student / Postdoc who would apply machine learning to substance addiction research. The successful candidate will have the opportunity to develop innovative and explainable machine/deep learning algorithms that can identify patterns and predictors of alcohol addiction and cannabis use disorder using structural brain MRI, Ecological Momentary Assessments (EMA), and psychometric questionnaires. A key aspect of this research will be accounting for confounding variables, such as age or comorbidities, to ensure robust and reliable results. This project is part of the TRR265 research consortium (https://www.trr265.org/en) The position will be in the lab of Prof. Dr. rer. nat. Kerstin Ritter (https://psychiatrie-psychotherapie.charite.de/en/research/translation_and_n…) Salary grade: TV-L E13 (100%) Starting date: August 01, 2023, for ~ 4 years Soft application deadline: June 25th, 2023 The position would remain open until filled. Qualifications: - Master’s degree with excellent grades in Computer Science, Data Science, Statistics, Physics, Computational Neuroscience or a related field - Experience with data analysis, visualization, and developing machine learning algorithms - Strong programming skills in Python and PyTorch, and experience working with linux servers and GitHub - Some prior experience with publishing research papers and working independently on open research questions - Excellent written and oral communication skills Ideal additional qualifications: - Familiarity with developing explainable deep learning algorithms and benchmarking model performance - Prior experience with psychiatric research - Prior experience with neuroimaging - Familiarity with analyzing healthcare data such as ecological momentary assessments and psychometric questionnaires -Prior experience with publishing open-source research code To apply, please submit: CV with contact information of 2-3 references Short motivation letter (max 1 page) mentioning the skills you can bring to this project Master’s / PhD degree transcript (if available) Please send your application asap to Roshan Rane (roshan.rane(a)bccn-berlin.de <mailto:roshan.rane@charite.de>) and Kerstin Ritter (kerstin.ritter(a)charite.de <mailto:kerstin.ritter@charite.de>). _____________________________________________ Looking forward to your applications! ---- With warm regards, Roshan Rane

June 21, 2023