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Brain Science

Enterprise Knowledge Hub for Brain Image Assessments

Focused on the brain as organ involved in neuropathologies and mental health this research area combines multi-modal brain imaging with omics methods and clinical assessments.

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The breadth and complexity of both, the affected organ and the effects requires multi-disciplinary collaborations of clinicians and researchers from psychiatry, neuroimaging, systems biology, neuro- and bioinformatics.

These aim to develop improved understanding of mechanisms, discovery and validate new multi-modal markers for diagnosis, prognosis, therapy assignment, stratification and monitoring, and translate these discoveries into clinical benefit for patients.

Our projects

EU and national research projects

LabVantage-Biomax contributes to Brain Science research in multiple previous and ongoing large-scale EU and national research projects from epilepsy to multiple sclerosis, dementia and alzheimer’s disease, psychosis and depression. Importantly, LabVantage-Biomax has been selected to provide a central infrastructure to the Human Brain Project. In these projects we provide secure and sustainable infrastructure that semantically integrate

Multi-modal neuroimaging data (sMRI, DTI, fMRI, EEG; MEG, PET)
Multiple brain atlases and brain mappings
Imaging derived and omics data from allied consortia and public databases
Image and data analysis pipelines and workflows
Clinical data from different studies and disciplines

Areas and projects

( Click on a project to learn more )

MS-CONNECT is a bioinformatics platform to support clinical decision making in neurology. MS-CONNECT allows the in-depth analysis of changes in neural ‘wiring’ in the brain (connectomics). It is based on LabVantage-Biomax’ existing NeuroXM platform, that offers secure patient data management and analysis (artificial intelligence) of brain data.

METSY focused on schizophrenia and the association with metabolic syndrome by applying network analysis and machine learning to clinical, neuroimaging and metabolomics data. In DEVoTED LabVantage-Biomax and the Max-Plank Institute for Psychiatry developed a clinical decision support system for depression treatment response prediction using clinical data as well as genetic and omics factors. In TranSyS both partners expands this approach to multi-modal neuroimaging data (s/fMRI, DTI). LabVantage-Biomax applies its image analysis pipeline and multi-modal brain data integration while the MPIP contributes study design, study data and machine learning approaches.

One of the major cost factors in diagnosing sleep disorders is the manual scoring of several hours of nightly polysomnography data. SPAS aims to develop an adaptive machine learning assistant that can be trained by sleep labs to follow their preferred scoring routine and reduce the manual burden. LabVantage-Biomax provides the management for clinical, diagnostic and polysomnography data as well as the user interface to deliver the machine learning results into the sleep lab routine.

The Neuro-CONNECT projects as part of the Human Brain Project (HBP) develops the knowledge management solution for the HPB EBRAINS digital research infrastructure. LabVantage-Biomax applies its NeuroXM^™ technology to represents connectome information not only in image space but for the first time ever also in a unifying feature space. In feature space a full semantic integration of highly complex connectome data from any brain imaging modality and resolution becomes for the first time feasible. Moreover it allows to integrate ontologies to this feature space in order to put connectome information in its correct anatomical and functional context. In addition every connectome dataset is semantically integrated with the underlying brain atlas used for image parcellation into one compelling brain science knowledge model. In this way additional data such as omics measurements can be mapped to individual level structural and functional information.

Scientists from the Universities of Nottingham, Newcastle, Qingdao, Shanghai and Munich have studied the change in the connectome in drug-resistant epilepsy patients, using LabVantage-Biomax Informatics’ NeuroXM knowledge management platform. They discovered that connectivity between and within brain regions can be a precise predictor for disease progression and epilepsy surgery outcome.

The NeuroXM Brain Science Suite of LabVantage-Biomax was used to develop a knowledge model for high-resolution intra-areal connectivity with more than 50,000 cortical nodes and several million connections, as well as corresponding automated processing pipelines. This connectivity network could then be visualized and accessed via the web portal of NICARA™, the neuroimaging solution offered by LabVantage-Biomax. “Our experience shows us that our software can be easily deployed in hospitals,” explained project leader Dr. Markus Butz-Ostendorf of LabVantage-Biomax. “In addition, it can also be combined with other data from genetics or from other imaging approaches such as PET, CT or EEG.”

Dr. Marcus Kaiser, Professor of Neuroinformatics at the University of Nottingham, confirms, “The use of NeuroXM and NICARA is central to this research project. With the help of this advanced neuroimaging solution, we can analyze and evaluate the changes in the local network within brain regions and thus assess whether surgery will be successful or not.”

The results from this study have now been published in the journal Human Brain Mapping and high resolution connectomes in NICARA made it on the cover journal.

Our contribution

For a neurologist the availability of detailed, structural, functional and molecular information about a patient is overwhelming and requires computational support. At the same time research in Brain Sciences is based on multi-disciplinary collaboration to accumulate and make sense of the required diversity of information. This accumulation of complex data on multiple levels and the need for reproducible image analysis pipelines and integrative analysis brings exciting novel opportunities and challenges for IT-infrastructures.

One challenge on the technological side is to provide semantic, syntactic and technical interoperability of data, data bases, analytical and simulation software. At the same time the results these tools provide need to be combined into a graphical user interface that enable scientist, clinical researchers and clinicians to distil the integrated information into actionable knowledge and make use of it.

Providing NeuroXM™

Providing NeuroXM™ Brain Science Suite

LabVantage-Biomax provides the NeuroXM Brain Science Suite in Brain Science projects to integrate existing knowledge as dense graph, identify context specific layers of data and metadata and sub-graphs and map complex clinical, molecular (multi-omics), imaging and environmental data to generate dedicated knowledge bases for analysis and computational modelling. NeuroXM makes use of latest metadata standards such as OpenMinds and is fully compatible with the Knowledge Graph of the Human Brain Project/EBRAINS.

The unique semantic mapping between multiple brain atlases and the unifying feature space enables the integration of multiple imaging modalities with molecular data. In addition NeuroXM provides the technical interoperability to enable experts for data analysis and machine learning to programmatically access and use the integrated knowledge and data.

Standards and certifications

Supporting clinical research privacy tasks
(GDPR, ISO 9001, ISO 27001)

LabVantage-Biomax is ISO 9001 and ISO 27001 certified and applies the corresponding procedures of quality management and IT-security. The NeuroXM^TM Brain Science Suite provides encrypted data transfer, authentication, detailed access control based on resources and roles and full audit.

All technological and organisational measures required by the GDPR are implemented.

GDPR compatible data processing agreement templates are available and corresponding contracts have been approved by company and clinical data protection officers in major European countries.

The ISO 9001 based quality management ensures consistence between specification and reported result, including reviews of requirements and technical specifications, software implementation and documentation.

Quality assessment according to ISO 29119 includes unit, integration, regression and acceptance testing.

Fair data

Ensuring FAIR data
from experimental to computational

LabVantage-Biomax provides the NeuroXM Brain Science Suite as technological framework and its data scientist semantic modelling expertise to generate the interoperable Knowledge Base that provides access to data sources, data analysis tools and computational modelling. In addition we provide data harmonisation, literature mining and data quality services and thereby contributes to a world with more sustainable data. LabVantage-Biomax further supports the development of new neurodata standards as industry partner of the International NeuroInformatics Coordination Facility (INCF).

Generic NeuroXM knowledge model dedicated to neurodata. New components can be added for any data modality and can be connected to existing concepts semantically as easy as putting Lego bricks onto each other. By the help of NeuroXM, the knowledge model orchestrates database storage and retrieval of neurodata and makes complex multimodal data integration in neuroscience manageable.

Scientific background

Modern brain science goes beyond individual types of measurements and similar to research in Systems Medicine aims to connect functional and structural as well as molecular information.

In complex neuropathologies such as Multiple sclerosis and in psychiatric disease the approaches focused on a single data type such as structural MRI (sMRI) or genetics provide little explanatory and predicitve power regarding the patient functioning.

Therefore, methods to combine information from multiple data modalities are urgently needed. The field of connectomics (the “wiring” of the brain) is such a method which holds enormous value for clinical diagnostics as it connects functional and structural systems on a biological level.

From multiple sclerosis to depression, psychosis and sleep disorder a multitude of diseases and indications have been tackled in the Brain Science projects LabVantage-Biomax is or has been involved.

Partners and funding
Publications

Epilepsy

College of Control Science and Engineering, China University of Petroleum (East China), Qingdao Chin

School of Computing, Newcastle University, Newcastle upon Tyne UK

TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising Germany

NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham UK

Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham UK

School of Medicine, Shanghai Jiao Tong University, Shanghai China

DEVoTED

Max-Plank Institute for Psychiatry, Munich, Germany

Funding: Bavarian Ministry of Economy, Energy and Technology

METSY

VTT Technical Reasearch Centre of Finland, Teknologian Tutkimuskeskus, Helsinki, Finland

Madrid Health Service SERMAS Servicio Madrileno de Salud, Hospital General Universitario

University of Turku, Turun Yliopisto, Turku, Finland

THL National Institute for Health and Welfare, Terveyden ja Hyvinvoinnin Laitos, Helsinki, Finland

Philips Technologie GmbH, Hamburg, Germany

King’s College London, London, United Kingdom

Funding: EU FP7 framework

Neuro-CONNECT

152 Partner im Rahmen Human Brain Project

Funding: EU Horizon 2020 framework – Human Brain Project

SPAS

SWEZ Sleep-Wake-Epilepsy Center, Inselspital Bern, Bern, Switzerland

SUPSI University of Applied Sciences of Southern Switzerland, Lugano, Switzerland

Relitec, Nijkerk, Netherlands

Funding: Bundesministerium für Bildung und Forschung via Eurostars

TranSYS

https://h2020transys.eu/consortium/beneficiaries/

Funding: EU Horizon 2020 framework

Chen X, Wang Y, Kopetzky SJ, Butz-Ostendorf M, Kaiser M. Connectivity within regions characterizes epilepsy duration and treatment outcome. Hum Brain Mapp. 2021 Aug 15;42(12):3777–3791.
Kopetzky SJ, Butz-Ostendorf M. From Matrices to Knowledge: Using Semantic Networks to Annotate the Connectome. Front Neuroanat. 2018;12:111.Ammar A, Bonaretti S, Winckers L, Quik J, Bakker M, Maier D, Lynch I, van Rijn J, Willighagen E. A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. Nanomaterials. Multidisciplinary Digital Publishing Institute; 2020 Oct;10(10):2068. https://www.mdpi.com/2079-4991/10/10/2068
Frank E, Maier D, Pajula J, Suvitaival T, Borgan F, Butz-Ostendorf M, Fischer A, Hietala J, Howes O, Hyötyläinen T, Janssen J, Laurikainen H, Moreno C, Suvisaari J, Van Gils M, Orešič M. Platform for systems medicine research and diagnostic applications in psychotic disorders-The METSY project. Eur Psychiatry. 2018 Jan 17;
Arjen van Ooyen and Markus Butz-Ostendorf (Eds) The Rewiring Brain: A Computational Approach to Structural Plasticity in the Adult Brain. San Diego: Academic Press, 2017, ISBN 978-0-12-803784-3The Rewiring Brain

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