Human Brain Project Specific Grant Agreement 2

Rezultaty

D4.4.1 All Models of Key Cognitive Processes developed during SGA2

Presentation of all models developed by WP4.4 during the SGA2, including: functions and performance, validation (by SP4, by rest of the HBP and/or by third parties), how results compare to targeted impact, and links to models and related datasets in publicly accessible online repositories.

D2.4.1 Software tool for brain structure - phenotype associations

Software tool for brain structure - phenotype associations implemented (T2.4.2); software available for usage

D9.1.1 Working prototype of a Collaboratory app for graphical model building

Collaboratory app usable by an SP9 member outside the developer team

D5.6.1 Interactive classifier training via the new Viewer

Users can train machine learning algorithms interactively by giving annotations in the web-based Viewer (T5.6.1)

D2.6.1 Tool for Morphological classification of neurons

Tool for Morphological classification of neurons (T2.6.4) made available; storage of software on HBP Collab

D5.3.1 New release of interactive spatial alignment tool

We will deploy the 2nd release of the interactive spatial alignment tool started in SGA1. The release will provide a significantly streamlined user interface, especially a much better user experience in terms of landmark management and interactive navigation. (T5.3.3)

D7.3.1 Multi-compartment benchmark and validation suites on HPC systems

The validation and benchmark suites for multi- compartment simulators are deployed and their associated documentation can be downloaded from public repositories; the continuous integration framework is publishing up to date validation and benchmark results from HPC systems used in the HBP.

D9.5.1 Temporal filtering network

Network for temporal filtering running on SpiNNaker (Task 9.5.1)

D2.3.1 Alignment strategy of datasets from TPFM, 3D-PLI, and dMRI

Alignment strategy of datasets from TPFM, 3D-PLI, and dMRI implemented (T2.3.4); Datasets made available in the HBP human brain atlas

D9.3.1 PyNN 0.9 on SpiNNaker

As complete a PyNN 0.9 implementation on SpiNNaker as possible (Task 9.3.3)

D5.7.1 Representations of optical imaging data in the Neo data object model

This is a release of the Neo library that contains support for the representations of optical imaging data. This feature will facilitate the analysis of activity data obtained from optical imaging experiments using tools built on the Neo data model. Successful representation of a dataset in the Neo object model, and the subsequent application of an analysis function of the Elephant framework on that data object, will be shown (T5.7.1-2)

D4.3.1 All Models of Plasticity, Learning and Memory developed during SGA2

Presentation of all models developed by WP4.3 during the SGA2, including: functions and performance, validation (by SP4, by rest of the HBP and/or by third parties), how results compare to targeted impact, and links to models and related datasets in publicly accessible online repositories.

D4.5.1 All Whole-Brain Models developed during SGA2 and Comparison with Experiments

Presentation of all models developed by WP4.5 during the SGA2, including: functions and performance, validation (by SP4, by rest of the HBP and/or by third parties), how results compare to targeted impact, and links to models and related datasets in publicly accessible online repositories.

D2.1.1 Comparison of Deep-learning based cytoarchitectonic mapping of cortex in the big brain against gold standard cytoarchitectonic map

Deep-learning based cytoarchitectonic mapping of cortex in the big brain and comparison against gold standard cytoarchitectonic map (T2.1.4); map made available in the HBP human brain atlas

D8.5.3 Μedical Informatics Platform Releases - SOFTWARE & REPORT

Μedical Informatics Platform Releases - SOFTWARE & REPORT

D5.4.1 First release of software adapted to new Viewer Architecture

Coordinated release of several services related to atlas viewers, adapted to a more unified viewer infrastructure. The architecture of this unified viewer ecosystem will be specified by SP5 towards the end of SGA1 and become the basis for this work. (T5.4.3)

D4.2.1 All Models of Brain Circuits developed during SGA2

Presentation of all models developed by WP4.2 during the SGA2, including: functions and performance, validation (by SP4, by rest of the HBP and/or by third parties), how results compare to targeted impact, and links to models and related datasets in publicly accessible online repositories.

D4.1.1 All Models for Bridging Scales developed during

Presentation of all models developed by WP4.1 during the SGA2, including: functions and performance, validation (by SP4, by rest of the HBP and/or by third parties), how results compare to targeted impact, and links to models and related datasets in publicly accessible online repositories.

D6.1.1 SP6 Annual Compound Deliverable Year 1

Overview of key results and impact achieved in M1-M12, tailored for presentation to the relevant audiences (research/industry/public). References to HBP/SP/CDP objectives and use cases for navigation between multiple Subprojects. Linkage of results to components/a set of component factsheets (lower-level information: component ownership, technology readiness level, performed quality control checks, etc.).

D12.4.1 Data Policy Manual

Having a set of data-related policies is a requirement for the HBP in order to: -Ensure that expectations with regards to data handling are clear -Comply with all data-related regulations and legislation, in particular those related to data protection -Ensure that all data registered and used in the HBP comply with ethical and other requirements -Demonstrate good management and leadership and implement good practice in data management Milestone verified by upload of the Data Policy Manual.

D1.6.2 SP1 Mouse Brain Organisation and Interspecies Comparisons - Second Data Results package (update on implementation of the DMP - M24)

WPs involved: WP1.1, WP1.2, WP1.3, WP1.4, WP1.5, and WP1.6 Contents: final report on the SP1 planned deliveries. This report will include the datasets generated in the SGA2 on whole brain and four major brain circuits (neocortex, cerebellum, basal ganglia, and hippocampus) data. This report will also include the final results on the integration of molecular, cellular and functional data (neocortex, cerebellum, basal ganglia, and hippocampus) and its application for modelling.

D1.3.2 CDP1 Annual Compound Deliverable Year 2

CDP1 Annual Compound Deliverable Year 2 Overview of Key Results and Impact achieved in M13 to M24, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.)

D5.1.1 Completion of SGA1 data/model curation into NIP meta data database

Table showing link between data/model components in PLA and curated data/models in NIP (T5.1.1-2)

D8.6.1 CDP6 Results SGA2 Year 1 Implementation for accurate HPC-based screening protocols of neuro-drug candidates

CDP6 Results SGA2 Year 1 Implementation for accurate HPC-based screening protocols of neuro-drug candidates. CDP6 Annual compound deliverable Year 1 Overview of Key Results and Impact achieved in M1 to M12, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.) This deliverable will also refer to results for SGA2_HPC-based chemical optimisation codes and increasing ligand specificity toward receptors' subclasses

D12.5.2 SGA2 - SP12 M24 reporting (Component id: 2328)

Progress report SP12 M24 SGA2

D9.6.2 SP9 Neuromorphic Computing Platform - Results from SGA2 year 2

The summary of SP 9 results for project months M13-24, broken down by task. WPs involved: WP9.1, WP9.2, WP9.3, WP9.4, WP9.5 and WP9.6 In order to report fully, the Deliverable may need to include information that the SP does not wish to make public at the time of the report. This material will be included in the Deliverable for the EC and Reviewers, but not in the version published publicly.

D6.4.1 CDP2 Annual Compound Deliverable Year 2

Overview of key results and impact achieved in M13-M24, tailored for presentation to the relevant audiences (research/industry/public). References to HBP/SP/CDP objectives and use cases for navigation between multiple Subprojects. Linkage of results to components/a set of component factsheets (lower-level information: component ownership, technology readiness level, performed quality control checks, etc.).

D2.7.3 CDP3 Results for SGA2 Year 1

CDP3 SGA2 Results Overview Deliverable: Overview of Key Results achieved in M1 to M12, tailored for presentation to the relevant audiences (research/industry/public)

D3.1.1 Simultaneous 2-photon calcium imaging in dendritic tufts receiving feedback inputs, and cell bodies of the same neurons receiving feedforward inputs

Data collected and paper published. Cross-species comparisons in visual cortex incorporated. (T.3.1.2)

D10.5.2 SP10 Neurorobotics Platform - Results for SGA2 Year 2

WPs involved: WP10.1, WP10.2, WP10.3, WP10.4 & WP10.5 Summary of SP Results for M12-24, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications

D7.2.1 Key technologies for fast data access and retrieval

This report summarises key technologies to support fast data access and retrieval for interactive analysis and visualisation, which have been identified and tested. This deliverable does not yet comprise the final implementation of these technologies.

D12.3.2 2nd Report SP12-SGA2: Lessons from stakeholder engagement and dialogue

The report collects up on the lessons learned from stakeholder dialogue and engagement in the Human Brain Project, from the ramp-up to the end of the SGA2 phase, and it develops foundation for stakeholder engagement in the final phases of the Human Brain Project.

D11.5.1 Fourth HBP Curriculum teaching cycle released (T11.5.2)

Third HBP Curriculum teaching cycle through online questionnaire evaluated and online courses adapted. Fourth teaching cycle started and Call for Expression of Interest for HBP Curriculum Workshops announced. Evaluation results are made available for consortium members and the public upon request. Call for Expression of Interest announced to the scientific community.

D8.5.1 Software requirements specifications (SRS) - REPORT

Software requirements specifications (SRS) - REPORT

D6.3.1 SP6 Annual Compound Deliverable Year 2

D5.8.2 SP5 Neuroinformatics Platform - Results for SGA2 Year 2

Summary of SP Results for M13-24, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o CDP Products (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications NOTE: In order to report fully on the above topics, the Deliverable may need to include information that we would not wish to make public. This material will be included in the Deliverable for the EC and Reviewers, but not in the version published on the HBP public website.

D12.3.1 Report on SP12-SGA2 Citizen engagement

Report on citizen engagement activities across Europe, including recommendations from citizens to the Human Brain Project.

D8.4.1 Reports on disease signatures via sub-type identification, on development and application of methods, and tools

Report on identification of disease signatures and application development is delivered.

D5.2.1 Release of updated atlas curation supporting material

Users can access tutorials and SOPs from HBP workbench or request support from UiO atlas curation team (T5.2.2)

D5.8.1 SP5 Neuroinformatics Platform - Results for SGA2 Year 1

SP5 Neuroinformatics Platform - Results for SGA2 Year 1 Summary of SP Results for M1-12, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o CDP Products (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications o SP Roadmap for SGA2, validated by other SPs receiving inputs from your SP NOTE: In order to report fully on the above topics, the Deliverable may need to include information that we would not wish to make public. This material will be included in the Deliverable for the EC and Reviewers, but not in the version published on the HBP public website.

D8.3.1 Signed partnership with one European reference network

Signed partnership with one European reference network

D3.6.1 Systems and Cognitive Neuroscience - Results for SGA2 Year 1

WPs involved: WP3.1, WP3.2., WP3.3, WP3.4, WP3.5, WP3.6 Summary of SP3 Results for M1-12, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o CDP products (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications

D2.7.4 CDP3 Results for SGA2 Year 2

CDP3 SGA2 Results Overview Deliverable Overview of Key Results achieved in M13 to M24, tailored for presentation to the relevant audiences (research/industry/public)

D9.4.1 CDP5-Biological deep learning: Results for SGA2 Year 1

CDP5-Biological deep learning: Results for SGA2 Year 1 CDP5 Annual compound deliverable Year 1 Overview of Key Results and Impact achieved in M1 to M12, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.) This deliverable will be a public report including theoretical research on learning principles, their transfer to the HBP computing infrastructures in SP7 and SP9, results of initial experiments and plans for M13 to M24 in SGA2

D4.6.1 SP4 EITN activity report

Report on EITN activity, its success, points that can be improved and what is foreseen

D8.2.1 MIP installed in Thirty Hospitals

MIP installed in Thirty Hospitals Demonstration of MIP software installation in 30 hospitals. Demonstration will be in form of a summary report of results: data profiling in each site, issues and lessons learned, user tests and feedback received during the hand-over and training.

D5.10.1 CDP8 Results SGA2

CDP8 SGA2 Results Overview Deliverable: Overview of Key Results achieved in M1 to M24, tailored for presentation to the relevant audiences. WPs involved: WP5.10. Key results involved: KRc8.1, KRc8.2, KRc8.3. Use cases involved: SGA2-SP4-UC001, SGA2-SP5-UC001, SGA2-SP5-UC002, SGA2-SP6-UC001, SGA2-SP6-UC003, SGA2-SP7-UC001, SGA2-SP11-UC003. The report summarizes the results obtained during the project phase, which will involve: code for large-scale brain simulation on HBP’s Joint Platform; code for connectome extraction and integration of results into NIP ontology; interactive tutorials; preprocessed connectomes from major repositories; online version of von Economo and Koskinas atlas; linked connectivity to architectonic data; human connectivity predictions.

D1.6.3 SP1 Mouse Brain Organisation and Interspecies Comparisons - Comparative study of cells and microcircuits in the rodent and human brain

WPs involved: WP1.1, WP1.2, WP1.3, WP1.4, WP1.5, and WP1.6 Contents: report on the final comparative study of cells and microcircuits in the rodent and human brain.

D7.6.1 SP7 High-Performance Analytics and Computing Platform - Results for SGA2 Year 1

High Performance Analytics and Computing Platform v2.5. The Platform, accessible to end users through the HBP Collaboratory, will provide the HBP and the neuroscience community with access to federated data and scalable compute resources as well as visualisation and simulation technology.

D9.4.2 CDP5-Biological deep learning: Results for SGA2 Year 2

CDP5 Annual compound deliverable Year 2 Overview of Key Results and Impact achieved in M13 to M24, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.) This deliverable will be a public report including theoretical research on learning principles, their transfer to the HBP computing infrastructures in SP7 and SP9, final experimental results and applications, an evaluation of the developments outside the HBP and a planning outlook to SGA3.

D12.2.1 Report on conceptual issues in human identity

Report on conceptual issues in human identity.

D2.7.2 SP2 Human Brain Organisation - Results for SGA2 Year 2

WPs involved: WP2.1, WP2.2., WP2.3, WP2.4, WP2.5, WP2.6 & WP2.7 Summary of SP Results for M13-24

D8.10.1 Provide operational MIP infrastructures to UKAACHEN and CHARITE

Provide operational MIP infrastructures to UKAACHEN (P73) and CHARITE (P122), to develop and implement a pathophysiological model for neurobehavioural symptom clustering. Test run and report of data analysis.

D7.6.2 SP7 High-Performance Analytics and Computing Platform - Results for SGA2 Year 2

High Performance Analytics and Computing Platform v3. The Platform, accessible to end users through the HBP Collaboratory, will provide the HBP and the neuroscience community with access to federated data and scalable compute resources. It will also provide visualisation and exascale-ready simulation technology.

D8.1.2 SP8 MIP - Results for SGA2 Year 2

SP8 MIP - Results for SGA2 period 2 SP8 Summary of Results for M12-24: actual vs. planned results o Risks and Issues log updated o Key Results, Impact status & Exceptional Achievements (from users' perspective) o Dependent results flow (i.e. if/how dependent components were incorporated into the next) o Milestones due and achieved, how validated, by whom o Milestones due but not achieved, why, impact, corrective action o Lessons Learned (and if any incorporated already) o Product Roadmap updated o Platform User feedback on the period o Publications

D6.2.1 CDP2 Annual Compound Deliverable Year 1

D1.6.1 SP1 Mouse Brain Organisation and Interspecies Comparisons: First Data Results package (update on implementation of the DMP - M12)

WPs involved: WP1.1, WP1.2, WP1.3, WP1.4, WP1.5, and WP1.6 Contents: First report including the preliminary list of deliveries for the period M01-M12 including datasets, tools, and models. The results expected to be included are as follows: preliminary datasets generated in the SGA2 on whole brain and four major brain circuits (neocortex, cerebellum, basal ganglia, hippocampus); First draft on the integration of molecular, cellular and functional data (neocortex, cerebellum, basal ganglia, hippocampus) and its application for modelling; Preliminary datasets for the comparative study of cells and microcircuits in the rodent and human brain.

D8.1.1 SP8 MIP - Results for SGA2 Year 1

SP8 MIP - Results for SGA2 period 1 SP8 Summary of Results for M1-12: actual vs. planned results o Risks and Issues log updated o Key Results, Impact status & Exceptional Achievements (from users' perspective) o Dependent results flow (i.e. if/how dependent components were incorporated into the next) o Milestones due and achieved, how validated, by whom o Milestones due but not achieved, why, impact, corrective action o Lessons Learned (and if any incorporated already) o Product Roadmap updated o Platform User feedback on the period o Publications

D11.1.1 Governance handbook

DIR handbook with procedures to follow regarding internal management, interactions with PCO, with SP Leaders and with Advisory Boards. (T11.1.2)

D12.1.1 SP12-SGA2 Foresight Lab & Researchers Awareness background report 2

Original research: Briefing report on Communities and Infrastructure Building. Milestone verified by upload of the report.

D11.2.10 Gender Action Plan

The Gender Action Plan is a required reference document to align structure and processes, objectives and key activities for improved gender equality in HBP with DIR, SIB, GAC, Ethic Board, Education Programme and Subprojects.

D12.5.3 SGA2-SP12 Communication reporting (Component id: 2329)

Communication report SP12 M24 SGA2

D11.1.3 SP11 Management and Coordination – Public Key Results Year 2

Summary of SP11 public Key Results for SGA2 Year 2 (M13-M24)

D10.5.1 SP10 Neurorobotics Platform - Results for SGA2 Year 1

WPs involved: WP10.1, WP10.2, WP10.3, WP10.4 & WP10.5 Summary of SP Results for M1-12, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications o SP Roadmap for SGA3

D12.5.4 SP12 Opinion 3 (Component id: 1967)

SP12's third Opinion on ethical, philosophical and societal issues related to consciousness. (ID: 1967)

D2.2.1 CDP4 Visuo-Motor Integration - Results for SGA2 Year 1

CDP4 Annual compound deliverable Year 1 Overview of Key Results and Impact achieved in M1 to M12, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.)

D11.3.4 Short Summary of Infrastructure Voucher Programme

Infrastructure Vouchers calls closed; vouchers assigned to the selected users; budget distribution made; short evaluation summary report (T11.3.4, T11.6.1)

D3.3.1 Acquisition of first datasets of electrophysiological recordings of hippocampal cells in VR environment

Release of software code and simulated data (preliminary version) (T3.2.5)

D12.5.1 SGA2-SP12 M12 reporting

Progress report of SP12 for M12 SGA2.

D9.6.1 SP9 Neuromorphic Computing Platform - Results from SGA2 year 1

The summary of SP 9 results for project months M1-12, broken down by task. WPs involved: WP9.1, WP9.2, WP9.3, WP9.4, WP9.5 and WP9.6 In order to report fully, the Deliverable may need to include information that the SP does not wish to make public at the time of the report. This material will be included in the Deliverable for the EC and Reviewers, but not in the version published publicly.

D7.1.1 HPAC Platform Architecture Specification v1

This report will contain a first specification within SGA2 of the HPAC Platform including the Fenix infrastructure.

D6.5.1 SP6 Summary Report on Community Outreach

Summary report of SP6 SGA2 community outreach.

D4.7.1 SP4 Theoretical Neuroscience models - 1st part

Involves all models of work done from all members of the SP4 during the 1st year of SGA2. As there are some models not yet published, there will be a confidential annex for this confidential data that will be only accessible to reviewers, EC and PCO.

D3.6.2 SP3 Systems and Cognitive Neuroscience - Results for SGA2 Year 2

WPs involved: WP3.1, WP3.2., WP3.3, WP3.4, WP3.5, WP3.6 Summary of SP3 Results for M13-24, broken down by Task: o Actual vs. planned results (due & done/due & not done) o Results passed to another Task, WP or SP (due & done/due & not done) o CDP products (due & done/due & not done) o Milestones due and achieved, how validated, by whom. o Milestones due but not achieved, why, impact, corrective action o Publications

D 1.3.1 CDP1 Annual Compound Deliverable Year 1

CDP1 Annual Compound Deliverable Year 1 Overview of Key Results and Impact achieved in M1 to M12, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.)

D5.9.1 Strategy and organization of a High-Level Support Team (HLST)

Plan for decision making on the use of resources to achieve the overall goals of the joint platform and organization and coordination of the operations of the HLST.

D4.4.2 CDP7 Results SGA2

This deliverable describes the results of CDP7during SGA2, focusing in particular on novel empirical and computational studies of hierarchical navigational planning in humans and rodents

D2.7.1 SP2 Human Brain Organisation - Results for SGA2 Year 1

WPs involved: WP2.1, WP2.2., WP2.3, WP2.4, WP2.5, WP2.6 & WP2.7 Summary of SP Results for M1-12

D2.5.1 CDP4 Visuo-Motor Integration - Results for SGA2 Year 2

CDP4 Annual compound deliverable Year 2 Overview of Key Results and Impact achieved in M13 to M24, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.)

D8.6.2 CDP6 Results SGA2 Year 2 HPC-based chemical optimisation codes increasing ligand specificity toward receptors' subclasses

CDP6 Annual compound deliverable Year 2 Overview of Key Results and Impact achieved in M13 to M24, tailored for presentation to the relevant audiences (research/industry/public) References to HBP/SP/CDP objectives and Use Cases for navigation between multiple Sub-Projects Linkage of Results to components/a set of component fact sheets (lower level information: Component ownership, Technology Readiness level, performed Quality Control checks, etc.) This deliverable will also refer to results for SGA2_HPC-based screening protocols and implementation for accurate HPC-based screening protocols of neuro-drug candidates.

D8.9.2 Curated and tested brain disease ontologies integrated within application services

Brain ontologies are integrated and accessible through OLS-NEURO. All application services (OLS-NEURO, SCAIView-Neuro) are online and available for use in MIP.

D8.7.2 BIDS Apps for imaging data processing pipelines

Applications for the imaging data processing pipelines using the Brain Imaging Data Structure format.

D5.5.1 Reproducible scientific software release 2

This production release will make publicly available JupyterLab functionality optimized and integrated with HBP data management solutions and data service APIs (T5.5.2)

D8.5.2 Μedical Informatics Platform Releases - SOFTWARE & REPORT

SOFTWARE & REPORT

D7.5.1 HPAC Platform including CEA resources

The compute and storage resources of the new HPAC partner CEA are integrated into the HPAC Platform, including the corresponding documentation in the Guidebook. The implementation of a use case workflow is used to demonstrate the functionality and documented in a short report.

D8.8.2 SEEGMIP database

DATA

D7.4.1 HBP Visualisation Software Catalogue

The HBP Visualisation Catalogue gives an overview of all visualisation tools and methods available in the HBP. It is a publicly available website that is also integrated into the Collaboratory. It contains semantic query functionality to support users in finding the right visualisation method and software for their specific needs.

Publikacje

Superficial white matter: A review on the dMRI analysis methods and applications

Autorzy: Miguel Guevara, Pamela Guevara, Claudio Román, Jean-François Mangin
Opublikowane w: NeuroImage, Numer 212, 2020, Strona(/y) 116673, ISSN 1053-8119
Wydawca: Academic Press
DOI: 10.1016/j.neuroimage.2020.116673

Unveiling the Synaptic Function and Structure Using Paired Recordings From Synaptically Coupled Neurons

Autorzy: Guanxiao Qi, Danqing Yang, Chao Ding, Dirk Feldmeyer
Opublikowane w: Frontiers in Synaptic Neuroscience, Numer 12, 2020, ISSN 1663-3563
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fnsyn.2020.00005

Multi-scale account of the network structure of macaque visual cortex

Autorzy: Maximilian Schmidt, Rembrandt Bakker, Claus C. Hilgetag, Markus Diesmann, Sacha J. van Albada
Opublikowane w: Brain Structure and Function, Numer 223/3, 2018, Strona(/y) 1409-1435, ISSN 1863-2653
Wydawca: Springer Verlag
DOI: 10.1007/s00429-017-1554-4

Cortical layers: Cyto-, myelo-, receptor- and synaptic architecture in human cortical areas

Autorzy: Nicola Palomero-Gallagher, Karl Zilles
Opublikowane w: NeuroImage, Numer 197, 2019, Strona(/y) 716-741, ISSN 1053-8119
Wydawca: Academic Press
DOI: 10.1016/j.neuroimage.2017.08.035

Mechanisms Underlying the Neuromodulation of Spinal Circuits for Correcting Gait and Balance Deficits after Spinal Cord Injury

Autorzy: Eduardo Martin Moraud, Marco Capogrosso, Emanuele Formento, Nikolaus Wenger, Jack DiGiovanna, Grégoire Courtine, Silvestro Micera
Opublikowane w: Neuron, Numer 89/4, 2016, Strona(/y) 814-828, ISSN 0896-6273
Wydawca: Cell Press
DOI: 10.1016/j.neuron.2016.01.009

Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling

Autorzy: Shigekazu Tabata, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, Shohei Uchinomiya, Harumi Harada, Makoto Itakura, Itaru Hamachi, Ryuichi Shigemoto, Akio Ojida
Opublikowane w: iScience, Numer 22, 2019, Strona(/y) 256-268, ISSN 2589-0042
Wydawca: Elsevier BV
DOI: 10.1016/j.isci.2019.11.025

Study of the Size and Shape of Synapses in the Juvenile Rat Somatosensory Cortex with 3D Electron Microscopy

Autorzy: Andrea Santuy, José-Rodrigo Rodríguez, Javier DeFelipe, Angel Merchán-Pérez
Opublikowane w: eneuro, Numer 5/1, 2018, Strona(/y) ENEURO.0377-17.2017, ISSN 2373-2822
Wydawca: Society for Neuroscience
DOI: 10.1523/eneuro.0377-17.2017

Demonstrating Advantages of Neuromorphic Computation: A Pilot Study

Autorzy: Timo Wunderlich, Akos F. Kungl, Eric Müller, Andreas Hartel, Yannik Stradmann, Syed Ahmed Aamir, Andreas Grübl, Arthur Heimbrecht, Korbinian Schreiber, David Stöckel, Christian Pehle, Sebastian Billaudelle, Gerd Kiene, Christian Mauch, Johannes Schemmel, Karlheinz Meier, Mihai A. Petrovici
Opublikowane w: Frontiers in Neuroscience, Numer 13, 2019, ISSN 1662-453X
Wydawca: Frontiers Media SA
DOI: 10.3389/fnins.2019.00260

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Multicontact Co-operativity in Spike-Timing–Dependent Structural Plasticity Stabilizes Networks

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Sleep-like slow oscillations improve visual classification through synaptic homeostasis and memory association in a thalamo-cortical model

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International Brain Initiative: An Innovative Framework for Coordinated Global Brain Research Efforts

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Mind Reading and Writing: The Future of Neurotechnology

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Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions

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Neuroethics Questions to Guide Ethical Research in the International Brain Initiatives

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Neuroethical and Social Implications of Using Transcranial Electrical Stimulation to Augment Creative Cognition

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An endogenous explanation of growth: direct-to-consumer stem cell therapies in PR China, India and the USA

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Dynamic Redistribution of Plasticity in a Cerebellar Spiking Neural Network Reproducing an Associative Learning Task Perturbed by TMS

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Benchmarking of Neuromorphic Hardware Systems

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A fixed point exponential function accelerator for a neuromorphic many-core system

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Profiling a Many-core Neuromorphic Platform

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Real-Time Cortical Simulations: Energy and Interconnect Scaling on Distributed Systems

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Arbor — A Morphologically-Detailed Neural Network Simulation Library for Contemporary High-Performance Computing Architectures

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IO Challenges for Human Brain Atlasing Using Deep Learning Methods - An In-Depth Analysis

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Exploring Vestibulo-Ocular Adaptation in a Closed-Loop Neuro-Robotic Experiment Using STDP. A Simulation Study

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DROM - Enabling Efficient and Effortless Malleability for Resource Managers

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Multi-Modal Motion Activation for Robot Control Using Spiking Neurons

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MPI+OpenMP Tasking Scalability for the Simulation of the Human Brain - Human Brain Project

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Learning to Reproduce Visually Similar Movements by Minimizing Event-Based Prediction Error

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Efficient Fault Tolerance Through Dynamic Node Replacement

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Controlling a Robot Arm for Target Reaching without Planning Using Spiking Neurons

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Network-on-chip evaluation for a novel neural architecture

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Approximate Fixed-Point Elementary Function Accelerator for the SpiNNaker-2 Neuromorphic Chip

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Benchmarking and Characterization of event-based Neuromorphic Hardware

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Tailoring SVM Inference for Resource-Efficient ECG-Based Epilepsy Monitors

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A Self-Learning Methodology for Epileptic Seizure Detection with Minimally-Supervised Edge Labeling

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Integrating clinical data from hospital databases

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Long short-term memory and learning-to-learn in networks of spiking neurons

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Work-in-Progress: Impact of Graph Partitioning on SNN Placement for a Multi-Core Neuromorphic Architecture

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Work-in-Progress: Multiple Alignment of Packet Sequences for Efficient Communication in a Many-Core Neuromorphic System

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Two Simple NeuroCognitive Associative Memory Models

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Non-Linear Motor Control by Local Learning in Spiking Neural Networks

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Deep Rewiring: Training Very Sparse Deep Networks

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Efficient Job Scheduling for Clusters with Shared Tiered Storage

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Meta-data management and quality control for the medical informatics platform

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Deep reinforcement learning in a time-continuous model

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Holistic Slowdown Driven Scheduling and Resource Management for Malleable Jobs

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Discovering Unexpected Local Nonlinear Interactions in Scientific Black-box Models

Autorzy: Michael Doron, Idan Segev, Dafna Shahaf
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ViTa-SLAM: A Bio-inspired Visuo-Tactile SLAM for Navigation while Interacting with Aliased Environments

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ViTa-SLAM: Biologically-Inspired Visuo-Tactile SLAM

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Event-based computation: Unsupervised elementary motion decomposition.

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Accelerated simulation of a neuronal population via mathematical model order reduction

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Motion Prediction of Virtual Patterns, Human Hand Motions and a simplified Hand Manipulation Task with Hierarchical Temporal Memory

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Integration of Paired Spiking Cerebellar Models for Voluntary Movement Adaptation in a Closed-Loop Neuro-Robotic Experiment. A Simulation Study

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Nonlinear scaling of resource allocation in sensory bottlenecks

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Directed Graph Placement for SNN Simulation into a multi-core GALS Architecture

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Efficient Bundled Spatial Range Queries

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Constraints on sequence processing speed in biological neuronal networks

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Structured motor exploration for adaptive learning-based tracking in soft robotic manipulators

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The OTree: Multidimensional Indexing with efficient data Sampling for HPC

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Projection-based order reduction of a nonlinear biophysical neuronal network model

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Quantification of fiber orientation uncertainty in polarized light imaging of the human brain

Autorzy: Daniel Schmitz, Thomas Lippert, Katrin Amunts, Markus Axer
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Microsaccades for asynchronous feature extraction with spiking networks

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The Collaborative Virtual Reality Neurorobotics Lab

Autorzy: Carl Matthes, Tim Weissker, Emmanouil Angelidis, Alexander Kulik, Stephan Beck, Andre Kunert, Anton Frolov, Sandro Weber, Adrian Kreskowski, Bernd Froehlich
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Rank Selection in Non-negative Matrix Factorization: systematic comparison and a new MAD metric

Autorzy: Laura Muzzarelli, Susanne Weis, Simon B. Eickhoff, Kaustubh R. Patil
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Multi-Ray Jumping: Comprehensible Group Navigation for Collocated Users in Immersive Virtual Reality

Autorzy: Tim Weissker, Alexander Kulik, Bernd Froehlich
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Obstacle Avoidance Using Stereo Vision and Deep Reinforcement Learning in an Animal-like Robot

Autorzy: Fuhai Ling, Alejandro Jimenez-Rodriguez, Tony J. Prescott
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When is an action caused from within? Quantifying the causal chain leading to actions in simulated agents

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A Graph Signal Processing Approach to Study High Density EEG Signals in Patients with Disorders of Consciousness

Autorzy: Sepehr Mortaheb, Jitka Annen, Camille Chatelle, Helena Cassol, Geraldine Martens, Aurore Thibaut, Olivia Gosseries, Steven Laureys
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Gaussian and Exponential Lateral Connectivity on Distributed Spiking Neural Network Simulation

Autorzy: Elena Pastorelli, Pier Stanislao Paolucci, Francesco Simula, Andrea Biagioni, Fabrizio Capuani, Paolo Cretaro, Giulia De Bonis, Francesca Lo Cicero, Alessandro Lonardo, Michele Martinelli, Luca Pontisso, Piero Vicini, Roberto Ammendola
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Fast and deep neuromorphic learning with first-spike coding

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Closed-loop experiments on the BrainScaleS-2 architecture

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An energy-based model of folded autoencoders for unsupervised learning in cortical hierarchies

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Mapping Deep Neural Networks on SpiNNaker2

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Deep reinforcement learning for time-continuous substrates

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Time- and Space-Efficient Spatial Data Analytics

Autorzy: Pavlovic, Mirjana
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Contributions to Bayesian network classifiers and interneuron classification

Autorzy: Bojan Mihaljevic
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Directional-linear Bayesian networks and applications in neuroscience

Autorzy: Ignacio Leguey Vitoriano
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Efficient Query Processing for Spatial and Temporal Data Exploration

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The place-cell representation of a four-room maze with changeable connectivity

Autorzy: Anyi Liu
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Exploring synaptic transmission and regulation in ionotropic receptors by molecular dynamics and computational electrophysiology

Autorzy: Adrien Cerdan
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Method development for co-simulation of electrical-chemical systems in Neuroscience

Autorzy: Ekaterina Brocke
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Brain, consciousness and disorders of consciousness at the intersection of neuroscience and philosophy

Autorzy: Michele Farisco
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Electrophysiological Markers of Consciousness: Measures of connectivity, complexity, and signal diversity in EEG for distinguishing between conscious and unconscious brain states

Autorzy: Bjørn Erik Juel
Opublikowane w: 2019
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PhD thesis: Device Variability in Synapses of Neuromorphic Circuits

Autorzy: Christoph Koke
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Timely and cost-efficient data exploration through adaptive tuning

Autorzy: Matthaios-Alexandros Olma
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Computational Models of Astrocytes and Astrocyte–Neuron Interactions: Characterization, Reproducibility, and Future Perspectives

Autorzy: Tiina Manninen, Riikka Havela, Marja-Leena Linne
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A Brain-Inspired Cognitive System that Mimics the Dynamics of Human Thought

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Extending Redescription Mining to Multiple Views

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Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks

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Learning Continuous Muscle Control for a Multi-joint Arm by Extending Proximal Policy Optimization with a Liquid State Machine

Autorzy: Juan Camilo Vasquez Tieck, Marin Vlastelica Pogančić, Jacques Kaiser, Arne Roennau, Marc-Oliver Gewaltig, Rüdiger Dillmann
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Microsaccades for Neuromorphic Stereo Vision

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The Synthetic Psychology of the Self

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A Deep Predictive Coding Network for Inferring Hierarchical Causes Underlying Sensory Inputs

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Calibration Method to Improve Transfer from Simulation to Quadruped Robots

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Understanding Interstate Competitiveness and International Security in European Dual-Use Research

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Whisker-RatSLAM Applied to 6D Object Identification and Spatial Localisation

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Unraveling Brain Modularity Through Slow Oscillations

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Streaming Live Neuronal Simulation Data into Visualization and Analysis

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Local Optimal Transport for Functional Brain Template Estimation

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Evaluating the Benefits of Key-Value Databases for Scientific Applications

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Brain-Inspired Hardware for Artificial Intelligence: Accelerated Learning in a Physical-Model Spiking Neural Network

Autorzy: Timo Wunderlich, Akos F. Kungl, Eric Müller, Johannes Schemmel, Mihai Petrovici
Opublikowane w: Artificial Neural Networks and Machine Learning – ICANN 2019: Theoretical Neural Computation - 28th International Conference on Artificial Neural Networks, Munich, Germany, September 17–19, 2019, Proceedings, Part I, Numer 11727, 2019, Strona(/y) 119-122, ISBN 978-3-030-30486-7
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-30487-4_10

Constraint Exploration of Convolutional Network Architectures with Neuroevolution

Autorzy: Jonas Dominik Homburg, Michael Adams, Michael Thies, Timo Korthals, Marc Hesse, Ulrich Rückert
Opublikowane w: Advances in Computational Intelligence - 15th International Work-Conference on Artificial Neural Networks, IWANN 2019, Gran Canaria, Spain, June 12-14, 2019, Proceedings, Part II, Numer 11507, 2019, Strona(/y) 735-746, ISBN 978-3-030-20517-1
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-20518-8_61

Closed Loop Control of a Compliant Quadruped with Spiking Neural Networks

Autorzy: Alexander Vandesompele, Gabriel Urbain, Francis Wyffels, Joni Dambre
Opublikowane w: Biologically Inspired Cognitive Architectures 2019 - Proceedings of the Tenth Annual Meeting of the BICA Society, Numer 948, 2020, Strona(/y) 547-555, ISBN 978-3-030-25718-7
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-25719-4_71

Efficient Construction of Geometric Nerve Fiber Models for Simulation with 3D-PLI

Autorzy: Jan A. Reuter, Felix Matuschke, Nicole Schubert, Markus Axer
Opublikowane w: Bildverarbeitung für die Medizin 2019 - Algorithmen – Systeme – Anwendungen. Proceedings des Workshops vom 17. bis 19. März 2019 in Lübeck, 2019, Strona(/y) 333-338, ISBN 978-3-658-25325-7
Wydawca: Springer Fachmedien Wiesbaden
DOI: 10.1007/978-3-658-25326-4_73

Towards 3D Reconstruction of Neuronal Cell Distributions from Histological Human Brain Sections

Autorzy: Timo Dickscheid, Sarah Haas, Sebastian Bludau, Philipp Glock, Marcel Huysegoms, Katrin Amunts
Opublikowane w: 2019, ISBN 978-1-61499-998-0
Wydawca: IOS Press
DOI: 10.3233/apc190016

3D Polarized Light Imaging Portrayed: Visualization of Fiber Architecture Derived from 3D-PLI

Autorzy: Nicole Schubert, Markus Axer, Uwe Pietrzyk, Katrin Amunts
Opublikowane w: High-Resolution Neuroimaging - Basic Physical Principles and Clinical Applications, 2018, ISBN 978-953-51-3865-5
Wydawca: InTech
DOI: 10.5772/intechopen.72532

Intelligence Science II - Third IFIP TC 12 International Conference, ICIS 2018, Beijing, China, November 2-5, 2018, Proceedings

Autorzy: Zhongzhi ShiCyriel PennartzTiejun Huang
Opublikowane w: Intelligence Science II,, 2018, ISBN 978-3-030-01313-4
Wydawca: Springer, Cham
DOI: 10.1007/978-3-030-01313-4

2nd HBP Student Conference- Transdisciplinary Research Linking Neuroscience, Brain Medicine and Computer Science - Book of Abstracts

Autorzy: A. Santuy, N. Simidjievski, M. Armendariz, P. Bogdan, C. Canova, C. Modenato, A. Mosinska
Opublikowane w: 2019
Wydawca: Frontiers Media SA
DOI: 10.3389/978-2-88945-588-1

Ethics in Innovation Management as Meta-Responsibility: The Practice of Responsible Research and Innovation in Human Brain Simulation

Autorzy: Bernd Carsten Stahl, Jos Timmermans, Stephen Rainey, Mark Shaw
Opublikowane w: 2019
Wydawca: Routledge

SpiNNaker-A Spiking Neural Network Architecture

Autorzy: Steve Furber, Petrut Bogdan (editors)
Opublikowane w: 2020
Wydawca: Now Publishers Inc.
DOI: 10.1561/9781680836530

Control of Cardiac Function in vivo with a Light-Regulated Drug

Autorzy: Fabio Riefolo, Carlo Matera, Aida Garrido-Charles, Alexandre M. J. Gomila, Luca Agnetta, Enrique Claro, Roser Masgrau, Ulrike Holzgrabe, Montserrat Batlle, Michael Decker, Eduard Guasch, Pau Gorostiza
Opublikowane w: 2019
Wydawca: American Chemical Society (ACS)
DOI: 10.26434/chemrxiv.7472174.v1

Minimum Information for Neuroscience Data Sets (MINDS): The metadata standard of the Human Brain Project data sharing platform.

Autorzy: Zehl L, Zafarnia S, Köhnen S, Hilverling A, Andersson K, Legouée E, Hagen Blixhavn C, Aasebø IE, Puchades MA, Schlegel U, Kleven H, Schmid O, Gillespie T, Abrams MB, Davison A, Leergaard TB, Amunts K, Bjaalie JG, Dickscheid T
Opublikowane w: 2019
Wydawca: Neuroinformatics 2019
DOI: 10.12751/incf.ni2019.0068

The Limits of Dual Use

Autorzy: Mahfoud, Tara, Christine Aicardi, Saheli Datta, and Nikolas Rose
Opublikowane w: 2018
Wydawca: Issues in Science and Technology

Statistical field theory for neural networks

Autorzy: Moritz Helias, David Dahmen
Opublikowane w: 2019
Wydawca: ArXiv

Self-consistent formulations for stochastic nonlinear neuronal dynamics

Autorzy: Jonas Stapmanns, Tobias Kühn, David Dahmen, Thomas Luu, Carsten Honerkamp, Moritz Helias
Opublikowane w: 2018
Wydawca: arxiv

Dendritic cortical microcircuits approximate the backpropagation algorithm

Autorzy: João Sacramento, Rui Ponte Costa, Yoshua Bengio, Walter Senn
Opublikowane w: 2018
Wydawca: ArXiv

Contextual Encoder-Decoder Network for Visual Saliency Prediction

Autorzy: Kroner, A., Senden, M., Driessens, K., & Goebel, R.
Opublikowane w: 2019
Wydawca: ArXiv

Sizing the length of complex networks

Autorzy: G. Zamora-López & R. Brasselet
Opublikowane w: 2018
Wydawca: arxiv

Improving Spatial Data Processing by Clipping Minimum Bounding Boxes

Autorzy: Sidlauskas, Darius ; Sean Chester ; Tzirita Zacharatou, Eleni ; Ailamaki, Anastasia
Opublikowane w: 2018
Wydawca: EPFL

Biologically inspired alternatives to backpropagation through time for learning in recurrent neural nets

Autorzy: Guillaume Bellec, Franz Scherr, Elias Hajek , Darjan Salaj , Robert Legenstein , and Wolfgang Maass
Opublikowane w: 2019
Wydawca: arXIv Org

Reconciliation of weak pairwise spike-train correlations and highly co- herent local field potentials across space

Autorzy: Johanna Senk, Espen Hagen, Sacha J. van Albada, Markus Diesmann
Opublikowane w: 2018
Wydawca: na

A model for structured information representation in neural networks

Autorzy: Michael G. Müller, Christos H. Papadimitriou, Wolfgang Maass, Robert Legenstein
Opublikowane w: 2019
Wydawca: na

Multi-area-model

Autorzy: Schmidt M.
Opublikowane w: 2018
Wydawca: Github

Neurorobotic Mouse (NeRmo) V4.1

Autorzy: Lucas, P. ; Morin, F. O. ; Conradt, J. ; Knoll, A.
Opublikowane w: 2020
Wydawca: Technische Universität München
DOI: 10.14459/2020md1540519

Vorbild Natur. Wie Maschinen das Lernen lernen

Autorzy: Johannes Schemmel
Opublikowane w: 2019
Wydawca: Forschungsmagazin Ruperto Carola
DOI: 10.17885/heiup.ruca.2019.15.24099

Optogenetic vision restoration with high resolution

Autorzy: U. Ferrari, S. Deny, A. Sengupta, R. Caplette, J.A. Sahel, D. Dalkara, S. Picaud, J. Duebel, O. Marre
Opublikowane w: 2018
Wydawca: N/A
DOI: 10.1101/470773

Design of a Biomimetic Rodent Robot

Autorzy: Peer Lucas, Florian Walter, Alois Knoll
Opublikowane w: 2018
Wydawca: Technische Universität München, Institut für Informatik
DOI: 10.14459/2018md1464578

An efficient analytical reduction of nonlinear detailed neuron models

Autorzy: Oren Amsalem, Guy Eyal, Noa Rogozinski, Idan Segev
Opublikowane w: BioRxiv, 2018
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/506485

Whole-neuron synaptic mapping reveals local balance between excitatory and inhibitory synapse organization

Autorzy: Daniel Maxim Iascone, Yujie Li, Uygar Sumbul, Michael Doron, Hanbo Chen, Valentine Andreu, Finola Goudy, Idan Segev, Hanchuan Peng, Franck Polleux
Opublikowane w: 2018
Wydawca: Cold Spring Harbor Laborator
DOI: 10.1101/395384

A mesoscopic layered cortical network model for spiking activity and local field potentials

Autorzy: Johanna Senk, Espen Hagen, Sacha J. van Albada, Markus Diesmann
Opublikowane w: 2018
Wydawca: N/A
DOI: 10.12751/nncn.bc2018.0163

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