Ingrid Reiten

• Blixhavn, Camilla Hagen; Reiten, Ingrid; Kleven, Heidi; Øvsthus, Martin; Yates, Sharon Christine & Schlegel, Ulrike [Show all 11 contributors for this article] (2024). The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases. Frontiers in Neuroinformatics. 18. doi: 10.3389/fninf.2024.1284107. Full text in Research Archive Show summary

  Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.

• Geminiani, Alice; Kathrein, Judith; Yegenoglu, Alper; Vogel, Franziska; Armendariz, Marcelo & Ben-Zion, Ziv [Show all 27 contributors for this article] (2024). Interdisciplinary and Collaborative Training in Neuroscience: Insights from the Human Brain Project Education Programme. Neuroinformatics. ISSN 1539-2791. 22(4), p. 657–678. doi: 10.1007/s12021-024-09682-6. Full text in Research Archive Show summary

  Neuroscience education is challenged by rapidly evolving technology and the development of interdisciplinary approaches for brain research. The Human Brain Project (HBP) Education Programme aimed to address the need for interdisciplinary expertise in brain research by equipping a new generation of researchers with skills across neuroscience, medicine, and information technology. Over its ten year duration, the programme engaged over 1,300 experts and attracted more than 5,500 participants from various scientific disciplines in its blended learning curriculum, specialised schools and workshops, and events fostering dialogue among early-career researchers. Key principles of the programme’s approach included fostering interdisciplinarity, adaptability to the evolving research landscape and infrastructure, and a collaborative environment with a focus on empowering early-career researchers. Following the programme’s conclusion, we provide here an analysis and in-depth view across a diverse range of educational formats and events. Our results show that the Education Programme achieved success in its wide geographic reach, the diversity of participants, and the establishment of transversal collaborations. Building on these experiences and achievements, we describe how leveraging digital tools and platforms provides accessible and highly specialised training, which can enhance existing education programmes for the next generation of brain researchers working in decentralised European collaborative spaces. Finally, we present the lessons learnt so that similar initiatives may improve upon our experience and incorporate our suggestions into their own programme.

• Kleven, Heidi; Reiten, Ingrid; Blixhavn, Camilla Hagen; Schlegel, Ulrike; Øvsthus, Martin & Papp, Eszter Agnes [Show all 10 contributors for this article] (2023). A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting. Frontiers in Neuroinformatics. 17. doi: 10.3389/fninf.2023.1154080. Full text in Research Archive Show summary

  Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing.

• Dorman, Reinder; Bos, Jeroen J.; Vinck, Martin; Marchesi, Pietro; Fiorilli, Julien & Lorteije, Jeanette A M [Show all 10 contributors for this article] (2023). Spike-based coupling between single neurons and populations across rat sensory cortices, perirhinal cortex, and hippocampus. Cerebral Cortex. ISSN 1047-3211. 33(13), p. 8247–8264. doi: 10.1093/cercor/bhad111. Full text in Research Archive
• Reiten, Ingrid; Olsen, Grethe Mari; Bjaalie, Jan G.; Witter, Menno Peter & Leergaard, Trygve B. (2023). The efferent connections of theorbitofrontal, posterior parietal,and insular cortex of the rat brain. Scientific Data. 10(645), p. 1–17. doi: 10.1038/s41597-023-02527-y. Full text in Research Archive Show summary

  The orbitofrontal, posterior parietal, and insular cortices are sites of higher-order cognitive processing implicated in a wide range of behaviours, including working memory, attention guiding, decision making, and spatial navigation. To better understand how these regions contribute to such functions, we need detailed knowledge about the underlying structural connectivity. Several tract-tracing studies have investigated specific aspects of orbitofrontal, posterior parietal and insular connectivity, but a digital resource for studying the cortical and subcortical projections from these areas in detail is not available. We here present a comprehensive collection of brightfield and fluorescence microscopic images of serial coronal sections from 49 rat brain tract-tracing experiments, in which discrete injections of the anterograde tracers biotinylated dextran amine and/or Phaseolus vulgaris leucoagglutinin were placed in the orbitofrontal, parietal, or insular cortex. The images are spatially registered to the Waxholm Space Rat brain atlas. The image collection, with corresponding reference atlas maps, is suitable as a reference framework for investigating the brain-wide efferent connectivity of these cortical association areas.

• Fiorilli, Julien; Marchesi, Pietro; Ruikes, Thijs; Veld, Gerjan Huis in t; Buckton, Rhys & Reiten, Ingrid [Show all 8 contributors for this article] (2023). Neural correlates of object identity and reward outcome in the corticohippocampal hierarchy: double dissociation between perirhinal and secondary visual cortex. BioRxiv. ISSN 0362-4331. Full text in Research Archive
• Reiten, Ingrid; Uslu, Fazil Emre; Forè, Stèphanie; Pelgrims, Robbrecht; Ringers, Christa & Verdugo, Carmen Diaz [Show all 12 contributors for this article] (2017). Motile-cilia-mediated flow improves sensitivity and temporal resolution of olfactory computations. Current Biology. ISSN 0960-9822. 27(2), p. 166–174. doi: 10.1016/j.cub.2016.11.036. Full text in Research Archive Show summary

  Motile cilia are actively beating hair-like structures that cover the surface of multiple epithelia. The flow that ciliary beating generates is utilized for diverse functions and depends on the spatial location and biophysical properties of cilia. Here we show that the motile cilia in the nose of aquatic vertebrates are spatially organized and stably beat with an asymmetric pattern, resulting in a robust and stereotypical flow around the nose. Our results demonstrate that these flow fields attract odors to the nose pit and facilitate detection of odors by the olfactory system in stagnant environments. Moreover, we show that ciliary beating quickly exchanges the content of the nose, thereby improving the temporal resolution of the olfactory system for detecting dynamic changes of odor plumes in turbulent environments. Altogether, our work unravels a central function of ciliary beating for generating flow fields that increase the sensitivity and the temporal resolution of olfactory computations in the vertebrate brain.

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• Golla, Archana; Pieschnik, Sophia; Kobchenko, Maya; Reiten, Ingrid; Chatzopoulos, Serafeim & Rojas, César Parra [Show all 16 contributors for this article] (2026). Building an Integrated Scientific Knowledge Graph for Neuroscience: Enhancing Research Impact Analysis and Optimizing Data Curation. doi: 10.5281/ZENODO.18864403. Full text in Research Archive Show summary

  The Neuroscience pilot of the EU-funded SciLake project seeks to tackle the complexities of fragmented and disorganized open research data. This initiative has united partners with expertise in knowledge management with curators from EBRAINS (RRID: SCR_019260), an open research infrastructure focused on brain-related studies. The innovative Scientific Knowledge Graph (SKG) (https://bip.imsi.athenarc.gr/search/neuroscience-pilot) created through this pilot serves as a cohesive framework for data integration while enabling the use of value-added services provided by SciLake. The developed SKG combines curated datasets from EBRAINS with extensive neuroscience research products from the OpenAIRE neuroscience gateway (https://neuroscience.openaire.eu/). The SKG incorporates controlled terms from openMINDS (RRID: SCR_023173) as nodes and utilizes an entity recognition model to classify and map these terms in relevant texts, enriching the connections among research products. Additionally, the SciLake services deploy language models to extract mentions of research artifacts (RAs) and enhance the interlinking of research products. Fully integrated with impact-driven discovery and reproducibility tools and leveraging the analytical capabilities of SciLake, the SKG serves as a powerful resource for contextualizing curation efforts and exploring research trends, ultimately optimizing curation processes in the neuroscientific landscape.

• Benediktsdottir, Signy; Golla, Archana; Blixhavn, Camilla Hagen; Hennestad, Eivind; Kleven, Heidi & Najafi, Peyman [Show all 16 contributors for this article] (2024). Towards FAIR neuroscience: an efficient workflow for sharing and integrating data. Full text in Research Archive
• Reiten, Ingrid; Olsen, Grete; Bjaalie, Jan G.; Witter, Menno Peter & Leergaard, Trygve B. (2023). The efferent connections of the orbitofrontal, posterior parietal and insular cortices in the rat: FAIR tract tracing data enabled by EBRAINS. Full text in Research Archive Show summary

  Poster presenterer et datasett som er delt via EBRAINS (ebrains.eu). Datasettet inneholder bildemateriale av koronale rottehjernesnitt som er merket for anterograd tracer, samt en registerering av disse bildene til Waxholm Space Rat Brain v4 atlas. Dataene er delt i følge FAIR-prinsippene og er open access.

• Blixhavn, Camilla Hagen; Bjerke, Ingvild Elise; Reiten, Ingrid; Kleven, Heidi; Schlegel, Ulrike & Puchades, Maja [Show all 8 contributors for this article] (2023). A conceptual framework for positioning and integrating brain data in murine 3D brain atlases. Full text in Research Archive
• Pieschnik, Sophia; Golla, Archana; Reiten, Ingrid; Schlegel, Ulrike; Hennestad, Eivind & Hübenette, Saira Jameela [Show all 20 contributors for this article] (2023). Pioneering open neuroscience - the role of the curation services. Full text in Research Archive
• Reiten, Ingrid; Schlegel, Ulrike; Aasebø, Ida; Davison, Andrew P.; Zehl, Lyuba & Schmid, Oliver [Show all 10 contributors for this article] (2022). Share FAIR neuroscience data using the EBRAINS curation services. Full text in Research Archive
• Reiten, Ingrid (2022). EBRAINS Data and Knowledge Services: Perspectives on open data from within EBRAINS. Full text in Research Archive
• Reiten, Ingrid; Schlegel, Ulrike; Aasebø, Ida; Swieten, Maaike M. H. van; Davison, Andrew P. & Zehl, Lyuba [Show all 11 contributors for this article] (2022). Share FAIR neuroscience data using the EBRAINS curation services. Full text in Research Archive
• Puchades, Maja; Reiten, Ingrid; Destexhe, Alain; Palomero-Gallagher, Nicola; Ruikes, Thijs & Leergaard, Trygve B. [Show all 7 contributors for this article] (2022). Workshop: Towards exploration of disease mechanisms in animal models: atlases, analysis, modelling and simulation. Full text in Research Archive Show summary

  Researchers Maja A. Puchades and Prof Jan G. Bjaalie have organised a paralell session titled: "Towards exploration of disease mechanisms in animal models". Agenda: For the 90 min meeting: · Presentation of speakers · New directions in disease models research · EBRAINS atlases enabling animal model research · Tools and analytical workflows for data integration in atlases · Use of animal brain atlases for modelling of brain function · Connectivity rat data: tract-tracing use case · Connectivity rat data: electrophysiological tetrodes use case · Panel discussion

• Reiten, Ingrid & Bjaalie, Jan G. (2022). EBRAINS Data & Knowledge Services: perspectives on open data from within EBRAINS. Full text in Research Archive
• Reiten, Ingrid & Leergaard, Trygve Brauns (2022). Digitisation, sharing and atlas registration of tract tracing histological sections. Full text in Research Archive
• Reiten, Ingrid; Schlegel, Ulrike; Aasebø, Ida; Zehl, Lyuba; Blixhavn, Camilla Hagen & Davison, Andrew [Show all 17 contributors for this article] (2021). Data sharing via EBRAINS: why and how. Full text in Research Archive
• Reiten, Ingrid; Schlegel, Ulrike; Aasebø, Ida Elisabeth Jørgensen; Blixhavn, Camilla Hagen; Zehl, Lyuba & Kjelsberg, Kasper [Show all 13 contributors for this article] (2020). Neuroscience community-gains from data sharing through the EBRAINS infrastructure. Full text in Research Archive Show summary

  EBRAINS provides tools and services which can be used to address challenges in brain research and brain-inspired technology development. EBRAINS assists scientists to collect, analyse, share and integrate brain data, and to perform modeling and simulation of brain function. EBRAINS is delivered by the EU Flagship Human Brain Project. All tools and services in EBRAINS are available for researchers in Europe and globally through https://ebrains.eu. Here we exemplify the use of the platform in different neuroscientific projects. In particular, the ‘Data & Knowledge’ services in EBRAINS offer one of the most comprehensive services for sharing brain research data ranging in type as well as spatial and temporal scale. An extensive metadata curation process ensures a robust presentation of datasets, models and software via the EBRAINS Knowledge Graph (https://kg.ebrains.eu/search/), making the data Findable, Accessible, Interoperable and Reusable (FAIR). By describing data across modalities in a standardised way and integrating it into the same reference space, data can be compared, combined and analysed with tools and analytical workflows embedded in the platform. New data, and data derived from the analytical workflows, can be submitted to curation and added to the existing EBRAINS datasets. The interplay between datasets, models and software makes EBRAINS attractive as a platform for discovery based and hypothesis driven research.

• Schlegel, Ulrike; Reiten, Ingrid; Aasebø, Ida Elisabeth Jørgensen; Blixhavn, Camilla Hagen; Zehl, Lyuba & Kjelsberg, Kasper [Show all 13 contributors for this article] (2020). EBRAINS data sharing: benefits and workflow. Full text in Research Archive
• Reiten, Ingrid; Schlegel, Ulrike; Blixhavn, Camilla Hagen; Andersson, Krister Andreas; Aasebø, Ida Elisabeth Jørgensen & Yates, Sharon Christine [Show all 12 contributors for this article] (2020). Data sharing through the online EBRAINS platform: a new service for brain research. Full text in Research Archive Show summary

  Enhancing the reproducibility and transparency of research is an emerging theme across scientific disciplines, driven by new technological advances, and captured by the Open Science concept. The heterogeneity of research data, which often hinders direct comparisons of findings, adds a layer of complexity to this effort. To address these challenges in neuroscience, the Human Brain Project has developed a new research infrastructure, EBRAINS, providing tools and services to the neuroscientific community. The EBRAINS data curation service offers comprehensive stewardship for sharing experimental and computational data. New workflows and standards for neuroscience data and metadata management have been developed to make the research results discoverable, comparable across modalities, and possible to reanalyse and reuse in new combinations. Here we present our workflows and curation services tailored for sharing heterogeneous neuroscience data. We demonstrate the integration of such data in the infrastructure, and highlight some practicalities for researchers who want to share their neuroscience data through EBRAINS.

• Ringers, Christa; Hansen, Jan; Reiten, Ingrid; Pelgrims, Robbrecht; Yaksi, Emre & Jurisch-Yaksi, Nathalie (2018). The role of second messengers in the regulation of ciliary beating. Full text in Research Archive

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