Nicolaas Ervik Groeneboom

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Academic interests

Principal developer of Nutil (Neuroimaging Utilities), a tool for performing statistical analyses of rodent brain data.

Research interest keywords: Data analysis and statistics, real-time visualization, (OpenGL, Unity), 3D engine design, C++ and C#, procedural programming, computational cosmology, galaxy simulations, gravitational lensing, N-body simulations, halo finders, model testing and data fitting, Bayesian statistics, CMB and LSS anisotropies, modified Newtonian gravity, open source projects, ray tracing, compiler techniques, compiler optimisations, parsers and assemblers, low-level assembly generation, HPC and GPU programming (CUDA, GLSL).

Background

Various post-doc positions (2010,2012,2016)

Ph.D in astrophysics at the University of Oslo. Funded by the Research Council of Norway, 3 year grant. Completed in June 2010. Supervised by Hans Kristian Eriksen and Frode Hansen.

M.Sc. in theoretical astrophysics at the University of Oslo. Completed August 2007, supervised
by prof. Øystein Elgarøy.

B.Sc. Mathematics, University of Oslo, 2003-2006,

Full-time hobby programmer since 1986. 4 years of professional experience from the IT industry.

Creator and principal manager/developer of the open source project "TRSE", see https://www.turborascal.com (with more than 1000 users).

Tags: Nesys, Programmering, C++, Utvikler, Astrofysikk, Kosmologi

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.
Groeneboom, Nicolaas Ervik; Yates, Sharon Christine; Puchades, Maja & Bjaalie, Jan G. (2020). Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Frontiers in Neuroinformatics. ISSN 1662-5196. doi: 10.3389/fninf.2020.00037.
Yates, Sharon Christine; Groeneboom, Nicolaas Ervik; Coello, Christopher; Lichtenthaler, Stefan F.; Kuhn, Peer-Hendrik & Demuth, Hans-Ulrich [Show all 12 contributors for this article] (2019). QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Frontiers in Neuroinformatics. ISSN 1662-5196. 13. doi: 10.3389/fninf.2019.00075. Full text in Research Archive Show summary
Transgenic animal models are invaluable research tools for elucidating the pathways and mechanisms involved in the development of neurodegenerative diseases. Mechanistic clues can be revealed by applying labelling techniques such as immunohistochemistry or in situ hybridisation to brain tissue sections. Precision in both assigning anatomical location to the sections and quantifying labelled features is crucial for output validity, with a stereological approach or image-based feature extraction typically used. However, both approaches are restricted by the need to manually delineate anatomical regions. To circumvent this limitation, we present the QUINT workflow for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. The workflow is semi-automated, combining three open source software that can be operated without scripting knowledge, making it accessible to most researchers. As an example, a brain region-specific quantification of amyloid plaques across whole transgenic Tg2576 mouse brain series, immunohistochemically labelled for three amyloid-related antigens is demonstrated. First, the whole brain image series were registered to the Allen Mouse Brain Atlas to produce customised atlas maps adapted to match the cutting plan and proportions of the sections (QuickNII software). Second, the labelling was segmented from the original images by the Random Forest Algorithm for supervised classification (ilastik software). Finally, the segmented images and atlas maps were used to generate plaque quantifications for each region in the reference atlas (Nutil software). The method yielded comparable results to manual delineations and to the output of a stereological method. While the use case demonstrates the QUINT workflow for quantification of amyloid plaques only, the workflow is suited to all mouse or rat brain series with labelling that is visually distinct from the background, for example for the quantification of cells or labelled proteins.
Ade, Peter A.R.; Aghanim, N; Armitage-Caplan, C; Arnaud, M; Ashdown, M & Atrio-Barandela, F [Show all 276 contributors for this article] (2015). Planck 2013 results. XXXII. The updated Planck catalogue of Sunyaev-Zeldovich sources. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 581. doi: 10.1051/0004-6361/201525787. Full text in Research Archive
Ade, P. A. R.; Aghanim, N; Armitage-Caplan, C; Arnaud, M; Ashdown, M & Atrio-Barandela, F [Show all 274 contributors for this article] (2014). Planck 2013 results. XXIX. The Planck catalogue of Sunyaev-Zeldovich sources. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 571. doi: 10.1051/0004-6361/201321523. Full text in Research Archive
Groeneboom, Nicolaas Ervik & Dahle, Håkon (2014). INTRODUCING GAMER: A FAST AND ACCURATE METHOD FOR RAY-TRACING GALAXIES USING PROCEDURAL NOISE. The Astrophysical Journal (ApJ). ISSN 0004-637X. 783(2). doi: 10.1088/0004-637X/783/2/138. Full text in Research Archive
Dahle, Håkon; Gladders, M. D.; Sharon, K.; Bayliss, M. B.; Wuyts, E & Abramson, L. E. [Show all 14 contributors for this article] (2013). SDSS J2222+2745: A GRAVITATIONALLY LENSED SEXTUPLE QUASAR WITH A MAXIMUM IMAGE SEPARATION OF 15."1 DISCOVERED IN THE SLOAN GIANT ARCS SURVEY. The Astrophysical Journal (ApJ). ISSN 0004-637X. 773(2). doi: 10.1088/0004-637X/773/2/146. Full text in Research Archive
Groeneboom, Nicolaas Ervik; Ackerman, Lotty; Wehus, Ingunn Kathrine & Eriksen, Hans Kristian Kamfjord (2010). BAYESIAN ANALYSIS OF AN ANISOTROPIC UNIVERSE MODEL: SYSTEMATICS AND POLARIZATION. The Astrophysical Journal (ApJ). ISSN 0004-637X. 722(1), p. 452–459. doi: 10.1088/0004-637X/722/1/452.
Rudjord, Øystein; Groeneboom, Nicolaas Ervik; Hansen, Frode Kristian & Cabella, P. (2010). NON-GAUSSIANITIES IN THE LOCAL CURVATURE OF THE FIVE-YEAR WMAP DATA. The Astrophysical Journal (ApJ). ISSN 0004-637X. 718(1), p. 66–71. doi: 10.1088/0004-637X/718/1/66.
Hou, Zhen; Banday, Anthony J.; Górski, Krzysztof M.; Groeneboom, Nicolaas Ervik & Eriksen, Hans Kristian Kamfjord (2010). Frequentist comparison of CMB local extrema statistics in the five-year WMAP data with two anisotropic cosmological models. Monthly notices of the Royal Astronomical Society. ISSN 0035-8711. 401(4), p. 2379–2387. doi: 10.1111/j.1365-2966.2009.15866.x.
Groeneboom, Nicolaas Ervik & Eriksen, Hans Kristian Kamfjord (2009). BAYESIAN ANALYSIS OF SPARSE ANISOTROPIC UNIVERSE MODELS AND APPLICATION TO THE FIVE-YEAR WMAP DATA. The Astrophysical Journal (ApJ). ISSN 0004-637X. 690(2), p. 1807–1819. doi: 10.1088/0004-637X/690/2/1807.
Rudjord, Øystein; Groeneboom, Nicolaas Ervik; Eriksen, Hans Kristian Kamfjord; Huey, G.; Górski, Krzysztof M. & Jewell, J. B. (2009). COSMIC MICROWAVE BACKGROUND LIKELIHOOD APPROXIMATION BY A GAUSSIANIZED BLACKWELL-RAO ESTIMATOR. The Astrophysical Journal (ApJ). ISSN 0004-637X. 692(2), p. 1669–1677. doi: 10.1088/0004-637X/692/2/1669.
Groeneboom, Nicolaas Ervik; Eriksen, Hans Kristian Kamfjord; Górski, Krzysztof M.; Huey, G.; Jewell, J. B. & Wandelt, B (2009). BAYESIAN ANALYSIS OF WHITE NOISE LEVELS IN THE FIVE-YEAR WMAP DATA. The Astrophysical Journal (ApJ). ISSN 0004-637X. 702(1), p. L87–L90. doi: 10.1088/0004-637X/702/1/L87.
Wehus, Ingunn Kathrine; Ackerman, Lotty; Eriksen, Hans Kristian Kamfjord & Groeneboom, Nicolaas Ervik (2009). THE EFFECT OF ASYMMETRIC BEAMS IN THE WILKINSON MICROWAVE ANISOTROPY PROBE EXPERIMENT. The Astrophysical Journal (ApJ). ISSN 0004-637X. 707(1), p. 343–353. doi: 10.1088/0004-637X/707/1/343.
Groeneboom, Nicolaas Ervik & Elgarøy, Øystein (2008). Detection of trans-Planckian effects in the cosmic microwave background. Physical Review D. Particles and fields. ISSN 0556-2821. 77. doi: 10.1103/PhysRevD.77.043522.
Mota, David Fonseca; Kristiansen, Jostein Riiser; Koivisto, T & Groeneboom, Nicolaas Ervik (2007). Constraining dark energy anisotropic stress. Monthly notices of the Royal Astronomical Society. ISSN 0035-8711. 382, p. 793–800. doi: 10.1111/j.1365-2966.2007.12413.x.

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Yates, Sharon Christine; Gurdon, Brianna; Csucs, Gergely; Groeneboom, Nicolaas Ervik; Puchades, Maja Amedjkouh & Kaczorowski, Catherine [Show all 7 contributors for this article] (2023). High-throughput method for brain-wide characterisation of genetically diverse AD mice.
Yates, Sharon Christine; Gurdon, Brianna; Csucs, Gergely; Groeneboom, Nicolaas Ervik; Puchades, Maja Amedjkouh & Kaczorowski, Catherine [Show all 7 contributors for this article] (2022). Quint workflow for brain-wide quantification of rodent models: new functionality for high-throughput studies. Show summary
Sectioned brain tissue of rodent models is used to explore the cellular and molecular composition of the brain in health and disease. The QUINT workflow was developed to support standardized atlas-based analysis of sectioned tissue without the need for coding ability. It is shared on the EBRAINS Atlas Services as a suite of open-source tools that can be flexibly combined to meet the needs of diverse projects (ebrains.eu). This includes tools for atlas-registration, feature extraction and quantification in regions defined by a reference atlas of the brain. New functionality has been added to the QUINT workflow to meet the needs of a novel Alzheimer’s disease project involving a large population of genetically diverse mice, the AD-BDX panel (Neuner et al, Neuron 2019, PMID: 30595332). This includes QCAlign: a tool for assessing the quality of the section images, as well as the quality of the atlas-registration to the sections as performed with the registration tools. By supporting systematic assessment of the material, QCAlign allows the removal of damaged sections, and the post-processing of results according to strict criteria that are transparent and reproducible. As a proof-of-concept, the QCAlign tool was applied to data from the Alzheimer’s project to detect and remove sections with more than 30% damage. It was also used to assess the quality of the atlas-registration before and after application of nonlinear refinements to the registration. To summarize, QCAlign tackles challenges posed by high-throughput studies and expands the scope of the QUINT workflow for comprehensive analysis.
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.
Groeneboom, Nicolaas Ervik (2010). Searching for anomalies in the Cosmic Microwave Background. Unipub forlag. ISSN 1501-7710.

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Published June 2, 2021 12:33 PM - Last modified June 2, 2021 1:04 PM

Projects

Euclid