Heidi Kleven

• Gurdon, Brianna; Yates, Sharon Christine; Csucs, Gergely; Groeneboom, Nicolaas Ervik; Hadad, Niran & Telpoukhovskaia, Maria [Show all 19 contributors for this article] (2024). Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model. Communications Biology. ISSN 2399-3642. 7(1). doi: 10.1038/s42003-024-06242-1.
• 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. ISSN 1662-5196. 18. doi: 10.3389/fninf.2024.1284107.
• Kleven, Heidi; Gillespie, Thomas; Zehl, Lyuba; Dickscheid, Timo; Bjaalie, Jan G. & Maryann E., Martone [Show all 7 contributors for this article] (2023). AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Scientific Data. ISSN 2052-4463. 10(1). doi: 10.1038/s41597-023-02389-4. Full text in Research Archive
• Blixhavn, Camilla Hagen; Haug, Finn-Mogens Smejda; Kleven, Heidi; Puchades, Maja ; Bjaalie, Jan G. & Leergaard, Trygve B. (2023). A Timm-Nissl multiplane microscopic atlas of rat brain zincergic terminal fields and metal-containing glia. Scientific Data. ISSN 2052-4463. 10(150). doi: 10.1038/s41597-023-02012-6. Full text in Research Archive Show summary

  The ability of Timm’s sulphide silver method to stain zincergic terminal fields has made it a useful neuromorphological marker. Beyond its roles in zinc-signalling and neuromodulation, zinc is involved in the pathophysiology of ischemic stroke, epilepsy, degenerative diseases and neuropsychiatric conditions. In addition to visualising zincergic terminal fields, the method also labels transition metals in neuronal perikarya and glial cells. To provide a benchmark reference for planning and interpretation of experimental investigations of zinc-related phenomena in rat brains, we have established a comprehensive repository of serial microscopic images from a historical collection of coronally, horizontally and sagittally oriented rat brain sections stained with Timm’s method. Adjacent Nissl-stained sections showing cytoarchitecture, and customised atlas overlays from a three-dimensional rat brain reference atlas registered to each section image are included for spatial reference and guiding identification of anatomical boundaries. The Timm-Nissl atlas, available from EBRAINS, enables experimental researchers to navigate normal rat brain material in three planes and investigate the spatial distribution and density of zincergic terminal fields across the entire brain.

• 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. ISSN 1662-5196. 17. doi: 10.3389/fninf.2023.1154080. Full text in Research Archive
• Kleven, Heidi; Bjerke, Ingvild Elise; Clascá, Francisco; Groenewegen, Henk J.; Bjaalie, Jan G. & Leergaard, Trygve B. (2023). Waxholm Space atlas of the rat brain: A 3D atlas supporting data analysis and integration. Nature Methods. ISSN 1548-7091. 20, p. 1822–1829. doi: 10.1038/s41592-023-02034-3. Full text in Research Archive
• Gurdon, Brianna; Yates, Sharon Christine; Csucs, Gergely; Groeneboom, Nicolaas; Hadad, Niran & Telpoukhovskaia, Maria [Show all 19 contributors for this article] (2023). Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. bioRxiv. ISSN 2692-8205. doi: 10.1101/2023.02.27.530226.
• Jacobsen, Bente; Kleven, Heidi; Gatome, Wairimu; Las, Liora; Ulanovsky, Nachum & Witter, Menno Peter (2023). Organization of projections from the entorhinal cortex to the hippocampal formation of the Egyptian fruit bat Rousettus aegyptiacus. Hippocampus. ISSN 1050-9631. 33(8), p. 889–905. doi: 10.1002/hipo.23517. Full text in Research Archive
• Lillehaug, Sveinung; Yetman, Michael J.; Puchades, Maja ; Checinska, Martyna; Kleven, Heidi & Jankowsky, Joanna L. [Show all 8 contributors for this article] (2019). Data Descriptor: Brain-wide distribution of reporter expression in five transgenic tetracyclinetransactivator mouse lines. Scientific Data. ISSN 2052-4463. 6, p. 1–15. doi: 10.1038/sdata.2019.28.
• Bjerke, Ingvild Elise; Øvsthus, Martin; Andersson, Krister Andreas; Blixhavn, Camilla Hagen; Kleven, Heidi & Yates, Sharon Christine [Show all 9 contributors for this article] (2018). Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies. Frontiers in Neuroanatomy. ISSN 1662-5129. 12. doi: 10.3389/fnana.2018.00082. Full text in Research Archive
• Witter, Menno; Kleven, Heidi & Kobro-Flatmoen, Asgeir (2017). Comparative Contemplations on the Hippocampus. Brain, Behavior and Evolution. ISSN 0006-8977. 90(1), p. 15–24. doi: 10.1159/000475703. Full text in Research Archive

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• Kleven, Heidi; Øvsthus, Martin; Carey, Harry Alexander Chandler; Puchades, Maja ; Bjaalie, Jan G. & Leergaard, Trygve B. [Show all 7 contributors for this article] (2024). Three-dimensional reference atlases for integration and analysis of data from the postnatal mouse brain.
• Leergaard, Trygve B.; Puchades, Maja ; Kleven, Heidi & Bjerke, Ingvild Elise (2022). HBP Brain Matters webinar #12 "Rodent Brain Atlasing". Show summary

  This episode featured the following HBP researchers: Heidi Kleven who is a PhD student at the University of Oslo with a research focus on developing and expanding rat and mouse brain atlases. She presented her ongoing work on brain atlases, focusing on the Waxholm Space atlas of the Sprague Dawley rat brain. Maja Puchades from the University of Oslo presented an overview of EBRAINS tools for analyses of Rodent brain images. A pipeline consisting of several tools allows users to register their images to a reference atlas and perform quantitative analysis in an atlas context. Both standalone and online versions of the tools are now available through the EBRAINS infrastructure. Ingvild Bjerke from the University of Oslo is a postdoctoral researcher. Her research focuses on mapping cellular parameters in the rodent brain, using EBRAINS atlases and tools to perform brain-wide analyses. She presented her published research mapping calbindin- and parvalbumin-positive cells in the rat and mouse brain. The session was moderated by Trygve Leergaard who is a professor of Anatomy at the Institute of Basic Medical Sciences, University of Oslo. His research has been focused on resolving fundamental architectonical principles underlying brain map transformations in major sensorimotor projection systems connecting the cerebral cortex with several brain stem nuclei.

• Schlegel, Ulrike; Köhnen, Stefan; Davison, Andrew; Najafi, Peyman; Weyers, Benjamin & Gründling, Jan [Show all 16 contributors for this article] (2022). openMINDS - flexible metadata models for neuroscience. Show summary

  Enhancing transparency and findability of research data is an emerging theme across scientific disciplines. More and more journals and funders, such as the Research Council of Norway, require the sharing of data in accordance with the FAIR guiding principles (Wilkinson et al., Scientific Data 3:160018, 2016), but few publicly accessible databases achieve this requirement. Their suitability is determined by attributes and constraints of the underlying metadata model. In neuroscience, the heterogeneity of data is particularly challenging. The multimodal nature of the research data as well as the wide range in spatial and temporal scales need to be adequately captured. Therefore, a suitable metadata model for neuroscience data has to balance flexibility and restrictiveness to accommodate the individuality of research products, without diminishing comparability across them. Powered by the Human Brain Project (HBP) and EBRAINS, we present the open Metadata Initiative for Neuroscience Data Structures (openMINDS). This novel initiative develops and maintains interlinked metadata models tailored to describe neuroscience research products in graph databases, such as the EBRAINS Knowledge Graph. The openMINDS research products cover data originating from human, animal or simulation studies (datasets), computational models (models), software tools (software), formal specifications for structuring metadata and/or data (metaDataModels), and reference brain atlases (brainAtlas). To illustrate the power of openMINDS, we present selected features describing these research products. We highlight how respective data and their provenance as well as studied specimens can be captured with user-defined granularity, and how the various integration of data via openMINDS can enhance its comparability and findability within and beyond the EBRAINS Knowledge Graph.

• Blixhavn, Camilla Hagen; Finn-Mogens S., Haug; Kleven, Heidi; Puchades, Maja ; Bjaalie, Jan G. & Leergaard, Trygve B. (2022). Multiplane microscopic atlas of rat brain zincergic terminal fields and metal-containing glia stained with Timm's sulphide silver method.
• Schlegel, Ulrike; Köhnen, Stefan; Davison, Andrew P.; Najafi, Peyman; Weyers, Benjamin & Gründling, Jan [Show all 17 contributors for this article] (2021). openMINDS - flexible metadata models for neuroscience. Show summary

  Enhancing transparency and findability of research data is an emerging theme across scientific disciplines. While publicly accessible databases aid in achieving this goal, their suitability is determined by attributes and constraints of the underlying metadata model. In neuroscience, the heterogeneity of data is particularly challenging. The multimodal nature of the research data as well as the wide range in spatial and temporal scales need to be adequately captured . Therefore, a suitable metadata model for neuroscience data has to balance flexibility and restrictiveness to accommodate the individuality of research products, without diminishing comparability across them. Powered by the Human Brain Project (HBP) and EBRAINS, we present the open Metadata Initiative for Neuroscience Data Structures (openMINDS). This novel initiative develops and maintains interlinked metadata models tailored to describe neuroscience research products in graph databases, such as the EBRAINS Knowledge Graph. The openMINDS research products cover data originating from human, animal or simulation studies (datasets), computational models (models), software tools (software), formal specifications for structuring metadata and/or data (metaDataModels), and reference brain atlases (brainAtlas). To illustrate the power of openMINDS, we present selected features describing these research products. We highlight how respective data and their provenance as well as studied specimens can be captured with user-defined granularity, and how the various integration of data via openMINDS can enhance its comparability and findability within and beyond the EBRAINS Knowledge Graph.

• 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. 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.

• Andersson, Krister Andreas; Blixhavn, Camilla Hagen; Zehl, Lyuba; Zarfarnia, Sara; Köhnen, Stefan & Hilverling, Anna [Show all 19 contributors for this article] (2019). Resources for making neuroscience data FAIR. The Human Brain Project invites researchers to share, find, and use data via the new EBRAINS infrastructure.
• Andersson, Krister Andreas; Blixhavn, Camilla Hagen; Kleven, Heidi; Zehl, Lyuba; Bjerke, Ingvild Elise & Schmid, Oliver [Show all 17 contributors for this article] (2019). Neuroinformatics platform for making neuroscience data Findable, Accessible, Interoperable, and Reuseable.
• Andersson, Krister Andreas; Blixhavn, Camilla Hagen; Kleven, Heidi; Schlegel, Ulrike; Oliver, Schmid & Puchades, Maja [Show all 10 contributors for this article] (2019). EBRAINS fair data service: A novel infrastructure for making neuroscience data findable, accessible, interoperable, and reuseable.
• Blixhavn, Camilla Hagen; Andersson, Krister Andreas; Kleven, Heidi; Schlegel, Ulrike; Puchades, Maja & Bjaalie, Jan G. [Show all 7 contributors for this article] (2019). Find and explore rodent brain data using 3D atlases in the new EBRAINS infrastructure.
• Blixhavn, Camilla Hagen; Andersson, Krister Andreas; Kleven, Heidi; Schlegel, Ulrike; Puchades, Maja & Bjaalie, Jan G. [Show all 7 contributors for this article] (2019). Infrastructure and workflow for integrating and navigating multi-scale and multi-modal murine neuroscience data using 3D digital brain reference atlases.
• Schlegel, Ulrike; Blixhavn, Camilla Hagen; Andersson, Krister Andreas; Yates, Sharon Christine; Øvsthus, Martin & Bjerke, Ingvild Elise [Show all 11 contributors for this article] (2019). Integrating and analysing heterogeneous rodent neuroscience data using three-dimensional brain reference atlases. Show summary

  Achieving advances in the field of neuroscience with its rapidly growing number of published data requires integration across many scales and levels of investigation. Such integration is challenging due to the heterogeneous nature of the data, and the difficulty of comparing data from different studies. Key aspects include lack of standards for presentation of data and experimental parameters (metadata), and variable practices for assigning and reporting anatomical location in the brain. The EU Human Brain Project (HBP) is addressing these challenges by establishing an infrastructure of neuroinformatic tools and data curation services through which disparate neuroscience data can be shared, used and analysed. Three-dimensional (3D) open access brain reference atlases provide anatomical context for all the shared data, easing comparison and interpretation of findings. We here present HBP workflows for assigning metadata describing anatomical locations to different types of neuroscience data, and workflows for extracting, quantifying and co-visualizing morphological features from multiple datasets in 3D anatomical brain atlas viewers. We highlight the added value of mapping data to a common atlas framework in example studies, and demonstrate new analytic opportunities enabled by combining image analysis tools with information from a 3D brain reference atlas. The HBP now invites the community to use the new research infrastructure established.

• Andersson, Krister Andreas; Blixhavn, Camilla Hagen; Zehl, Lyuba; Markovic, Milica; Kleven, Heidi & Zafarnia, Sara [Show all 15 contributors for this article] (2018). HBP Curation service: Share your data via the Neuroinformatics platform.
• Zehl, Lyuba; Zafarnia, Sara; Köhnen, Stefan; Andersson, Krister Andreas; Markovic, Milica & Legouée, Elodie [Show all 20 contributors for this article] (2018). Integrating neuroscientific data into a unified database: from individual experiments to a standardized metadata collection using the Human Brain Project Neuroinformatics Platform.
• Zehl, Lyuba; Zafarnia, Sara; Köhnen, Stefan; Andersson, Krister Andreas; Markovic, Milica & Legouée, Elodie [Show all 20 contributors for this article] (2018). Integrating neuroscientific data into a unified database: from individual experiments to a standardized metadata collection using the Human Brain Project Neuroinformatics Platform.
• Blixhavn, Camilla Hagen; Andersson, Krister; Øvsthus, Martin; Bjerke, Ingvild Elise; Kleven, Heidi & Puchades, Maja [Show all 8 contributors for this article] (2018). Data integration through digital brain atlasing: Making diverse neuroscience data discoverable using Human Brain Project infrastructure.
• Imad, Jala; Kleven, Heidi; Clascá, Francisco; Wennberg, Arvind Eirik; Osen, Kirsten Kjelsberg & Coello, Sebastian Christopher [Show all 11 contributors for this article] (2017). Enriching and adding detail to the Waxholm Space rat brain reference atlas.
• Andersson, Krister Andreas; Bell, Simon; Bjerke, Ingvild Elise; Øvsthus, Martin; Blixhavn, Camilla Hagen & Kleven, Heidi [Show all 18 contributors for this article] (2017). Submitting data and metadata through the HBP Data Workbench: Concepts, data flows, policies, and best practices.
• Kleven, Heidi; Gatome, W; Las, L; Ulanovsky, N & Witter, Menno (2014). Organization of entorhinal-hippocampal projections in the Egyptian fruit bat.

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