Heidi Kleven

• Carey, Harry Alexander Chandler; Kleven, Heidi; Øvsthus, Martin; Yates, Sharon Christine; Csucs, Gergely & Puchades, Maja A. [Show all 10 contributors for this article] (2025). DeMBA: a developmental atlas for navigating the mouse brain in space and time. Nature Communications. 16. doi: 10.1038/s41467-025-63177-9. Full text in Research Archive Show summary

  Studies of the adult mouse brain have benefited from three-dimensional (3D) atlases providing standardised frameworks for data analysis and integration. However, few 3D atlases exist for the developing mouse brain, and none cover more than a few ages. This fails to represent the dynamic nature of development and is insufficient for researchers whose data fall between the ages of existent atlases. Existing atlases also neglect the spatial correspondence between ages, making comparison across ages difficult. We present the Developmental Mouse Brain Atlas (DeMBA), a 4D atlas encompassing every postnatal day from 4 to 56. DeMBA was created by using existing brain templates for six developmental time points and interpolating intermediate ages. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide the software package CCF translator, allowing coordinates or image volumes to be transformed between ages for comparison. These resources provide age-specific spatial frameworks incorporated in accessible analytic pipelines for developmental mouse brain data.

• Carey, Harry Alexander Chandler; Kleven, Heidi; Øvsthus, Martin; Yates, Sharon Christine; Csucs, Gergely & Puchades, Maja [Show all 9 contributors for this article] (2024). DeMBA: a developmental atlas for navigating the mouse brain in space and time. bioRxiv. ISSN 2692-8205. doi: 10.1101/2024.06.14.598876. Full text in Research Archive Show summary

  Studies of the adult mouse brain have benefited from three-dimensional (3D) atlases providing standardised frameworks for data analysis and integration. However, few 3D atlases exist for the developing mouse brain, and none cover more than a few ages. This fails to represent the dynamic nature of development and is insufficient for researchers whose data fall between the ages of existent atlases. Existing atlases also neglect the spatial correspondence between ages, making comparison across ages difficult. We present the Developmental Mouse Brain Atlas (DeMBA), a 4D atlas encompassing every postnatal day from 4 to 56. DeMBA was created by using existing brain templates for six developmental time points and interpolating intermediate ages. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide the software package CCF translator, allowing coordinates or image volumes to be transformed between ages for comparison. These resources provide age-specific spatial frameworks incorporated in accessible analytic pipelines for developmental mouse brain data.

• 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.

• 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. 7(1). doi: 10.1038/s42003-024-06242-1. Full text in Research Archive Show summary

  Alzheimer’s disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.

• Kleven, Heidi; Schlegel, Ulrike; Groenewegen, Henk J.; Leergaard, Trygve Brauns & Bjerke, Ingvild Elise (2024). Comparison of basal ganglia regions across murine brain atlases using metadata models and the Waxholm Space. Scientific Data. 11. doi: 10.1038/s41597-024-03863-3. Full text in Research Archive Show summary

  The murine basal ganglia regions are targets for research into complex brain functions such as motor control and habit formation. However, there are several ways to name and annotate these regions, posing challenges for interpretation and comparison of data across studies. Here, we give an overview of basal ganglia terms and boundaries in the literature and reference atlases, and describe the criteria used for annotating these regions in the Waxholm Space rat brain atlas. We go on to compare basal ganglia annotations in stereotaxic rat brain atlases and the Allen Mouse brain Common Coordinate Framework to those in the Waxholm Space rat brain atlas. We demonstrate and describe considerable differences in the terms and boundaries of most basal ganglia regions across atlases and their versions. We also register information about atlases and regions in the openMINDS metadata framework, facilitating integration of data in neuroscience databases. The comparisons of terms and boundaries across rat and mouse atlases support analysis and interpretation of existing and new data from the basal ganglia.

• 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.

• 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 Show summary

  Volumetric brain atlases are increasingly used to integrate and analyze diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present an update of the Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It provides a detailed map of the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fiber tracts. We document the criteria underlying the annotations and demonstrate how the atlas with related tools and workflows can be used to support interpretation, integration, analysis and dissemination of experimental rat brain data.

• 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 Show summary

  The hippocampal formation and entorhinal cortex are crucially involved in learning and memory as well as in spatial navigation. The conservation of these structures across the entire mammalian lineage demonstrates their importance. Information on a diverse set of spatially tuned neurons has become available, but we only have a rudimentary understanding of how anatomical network structure affects functional tuning. Bats are the only order of mammals that have evolved true flight, and with this specialization comes the need to navigate and behave in a three dimensional (3D) environment. Spatial tuning of cells in the entorhinal-hippocampal network of bats has been studied for some time, but whether the reported tuning in 3D is associated with changes in the entorhinal-hippocampal network is not known. Here we investigated the entorhinal-hippocampal projections in the Egyptian fruit bat (Rousettus aegyptiacus), by injecting chemical anterograde tracers in the entorhinal cortex. Detailed analyses of the terminations of these projections in the hippocampus showed that both the medial and lateral entorhinal cortex sent projections to the molecular layer of all subfields of the hippocampal formation. Our analyses showed that the terminal distributions of entorhinal fibers in the hippocampal formation of Egyptian fruit bats—including the proximo-distal and longitudinal topography and the layer-specificity—are similar to what has been described in other mammalian species such as rodents and primates. The major difference in entorhinal-hippocampal projections that was described to date between rodents and primates is in the terminal distribution of the DG projection. We found that bats have entorhinal-DG projections that seem more like those in primates than in rodents. It is likely that the latter projection in bats is specialized to the behavioral needs of this species, including 3D flight and long-distance navigation.

• Kleven, Heidi; Gillespie, Thomas; Zehl, Lyuba; Dickscheid, Timo; Bjaalie, Jan G. & E., Martone Maryann [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. 10(1). doi: 10.1038/s41597-023-02389-4. Full text in Research Archive Show summary

  Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.

• 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. 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. 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.

• 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. 6, p. 1–15. doi: 10.1038/sdata.2019.28. Full text in Research Archive
• 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. 12. doi: 10.3389/fnana.2018.00082. Full text in Research Archive Show summary

  In experimental neuroscientific research, anatomical location is a key attribute of experimental observations and critical for interpretation of results, replication of findings, and comparison of data across studies. With steadily rising numbers of publications reporting basic experimental results, there is an increasing need for integration and synthesis of data. Since comparison of data relies on consistently defined anatomical locations, it is a major concern that practices and precision in the reporting of location of observations from different types of experimental studies seem to vary considerably. To elucidate and possibly meet this challenge, we have evaluated and compared current practices for interpreting and documenting the anatomical location of measurements acquired from murine brains with different experimental methods. Our observations show substantial differences in approach, interpretation and reproducibility of anatomical locations among reports of different categories of experimental research, and strongly indicate that ambiguous reports of anatomical location can be attributed to missing descriptions. Based on these findings, we suggest a set of minimum requirements for documentation of anatomical location in experimental murine brain research. We furthermore demonstrate how these requirements have been applied in the EU Human Brain Project to optimize workflows for integration of heterogeneous data in common reference atlases. We propose broad adoption of some straightforward steps for improving the precision of location metadata and thereby facilitating interpretation, reuse and integration of data.

• 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 Show summary

  The hippocampus in mammals is a morphologically well-defined structure, and so are its main subdivisions. To define the homologous structure in other vertebrate clades, using these morphological criteria has been difficult, if not impossible, since the typical mammalian morphology is absent. Although there seems to be consensus that the most medial part of the pallium represents the hippocampus in all vertebrates, there is no consensus on whether all mammalian hippocampal subdivisions are present in the derivatives of the medial pallium in all vertebrate groups. The aim of this paper is to explore the potential relevance of connections to define the hippocampus across vertebrates, with a focus on mammals, reptiles, and birds.

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• Gonzales, Christina Martinez; Yates, Sharon Christine; Kleven, Heidi & Puchades, Maja (2026). From slices to 3D: QUINT workflow for brain atlas registration and image quantification. doi: https:/ebrains.eu/news-and-events/events/2026/from-slices-to-3d-quint-workflow-for-brain-atlas-registration-and-image. Full text in Research Archive Show summary

  This 1-hour online + Q&A roundtable brings together QUINT developers, experts in digital brain atlases and neuroinformatics, to discuss the QUINT Workflow. This event is designed for students and researchers working with histological images, offering a unique opportunity to ask questions and get feedback from leading experts in the field.

• Morabit, Oumnia; Kleven, Heidi; Giacometti, Camille; Palomero-Gallagher, Nicola & Leergaard, Trygve B. (2026). Anatomical subdivisions of the rat amygdaloid complex: an empirical basis for unifying MRI, DTI and histology-based boundary criteria in the Waxholm Space rat brain atlas. Full text in Research Archive Show summary

  The amygdaloid complex is part of the limbic system governing emotion, learning, implicit memory and social behaviour. Its implication in neuropsychiatric disease has motivated extensive experimental preclinical research in animal models, particularly in rodents and non-human primates. For investigations in rat models, the Waxholm Space (WHS) rat brain atlas provides three-dimensional standardized representations of brain regions and is increasingly used for data integration, spatial analysis, and comparisons across studies. While this atlas includes detailed delineations for most major brain structures, it lacks subdivisions of the amygdaloid complex. Addressing this, we have manually delineated nuclei of the rat amygdala on the basis of high-resolution structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) data, combined with co-registered cytoarchitectural, myeloarchitectural, and chemoarchitectural features derived from histological datasets. These multimodal data were interpreted and compared using available literature. We here present 3D delineations of the rat pallial and subpallial subdivisions of the amygdaloid complex, together with detailed documentation of delineation criteria. To facilitate cross-species translation, we also compared our delineation criteria and delineations to corresponding data from primates. This work represents an empirical basis for combining multimodal MRI and histological data to extend the anatomical delineations of the WHS rat brain atlas and to strengthen its role as a neuroinformatics resource for data integration, translational research, brain wide analyses and cross-species comparison particularly for future investigations into the neural mechanisms involving the amygdaloid complex. Funded from the European Union’s Research and Innovation Program Horizon Grant Agreement No. 101147319 (EBRAINS 2.0)

• Puchades, Maja; Bjerke, Ingvild Elise; Carey, Harry Alexander Chandler; Kleven, Heidi; Øvsthus, Martin & Yates, Sharon Christine [Show all 10 contributors for this article] (2025). QUINT workflow now supports whole brain analysis using the Developmental Mouse Brain Atlas (DeMBA). Full text in Research Archive Show summary

  INTRODUCTION: Three-dimensional, open access digital brain atlases are important resources in neuroscience research, opening new possibilities for automated analyses in atlas defined regions of interest. The EBRAINS QUINT workflow [1,2] has been developed to support standardized atlas-based analysis of sectioned tissue without the need for coding ability. It features integrated brain atlases for the adult rat and mouse brain and is increasingly used in the neuroscience community. However, a recurrent request from many QUINT users interested in understanding brain development, has been to include brain atlases representing different developmental ages, to so achieve better spatial registration for brains from young individuals. METHODS: To meet this need, we have now integrated the novel Developmental Mouse Brain Atlas (DeMBA), a four-dimensional atlas covering every postnatal day from 4 to 56 [3]. This atlas features segmentations from the widely adopted Allen Mouse Brain CCF and the Kim developmental atlases, that have been transformed and interpolated to the same ages, ensuring comparable region definitions across ages [4]. RESULTS AND DISCUSSION: The DeMBA atlas was implemented in the registration software QuickNII and VisuAlign and shared as specific packages together with the atlas itself on EBRAINS [4]. Those versions require usage of the specific Filebuilder utility shared within the packages. Next, the DeMBA atlas was implemented in a new Nutil Quantifier version (v1.1) and thereby the complete QUINT analysis can now be performed on young mouse brains. All the software tools and the DeMBA atlas are shared through the EBRAINS Knowledge graph [5]. We here present the updated QUINT workflow and give examples of preliminary developmental data analysis. References: 1.Yates, S. et al. (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13, 1–14. https://doi.org/10.3389/fninf.2019.00075 2. Puchades MA, Yates SC, Csucs G, Carey H, Balkir A, Leergaard TB and Bjaalie JG (2025) Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. Front. Neuroinform. 19:1629388. https://doi.org/10.3389/fninf.2025.1629388 3.Carey, H., Ovsthus, M., Kleven, H., Yates, S. C., Csucs, G., Puchades, M. A., Bjaalie, J. G., Leergaard, T. B., & Bjerke, I. E. (2024). Developmental mouse brain atlas (DeMBA) with continuous coverage of postnatal day 4 to 56 (v1) [Data set]. EBRAINS. https://doi.org/10.25493/V3AH-HK7 4.Carey, H., Kleven, H., Øvsthus, M. et al. DeMBA: a developmental atlas for navigating the mouse brain in space and time. Nat Commun 16, 8108 (2025). https://doi.org/10.1038/s41467-025-63177-9 5.https://search.kg.ebrains.eu Acknowledgeme

• 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
• 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. Full text in Research Archive
• 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
• 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. Full text in Research Archive 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; S., Haug Finn-Mogens; 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. Full text in Research Archive
• Leergaard, Trygve B.; Puchades, Maja; Kleven, Heidi & Bjerke, Ingvild Elise (2022). HBP Brain Matters webinar #12 "Rodent Brain Atlasing". Full text in Research Archive 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 P.; Najafi, Peyman; Weyers, Benjamin & Gründling, Jan [Show all 17 contributors for this article] (2021). openMINDS - flexible metadata models for neuroscience. Full text in Research Archive 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. 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.

• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive 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.

• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• Kleven, Heidi; Gatome, W; Las, L; Ulanovsky, N & Witter, Menno (2014). Organization of entorhinal-hippocampal projections in the Egyptian fruit bat. Full text in Research Archive

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