Academic interests
I combine my studies of the normal mouse brain development with neuroinformatics and digital atlasing. I am passionate about the open science movement and FAIR research, and make all data from my research public.
Expertise:
- Immunohistochemistry
- Image segmentation
- Cell counting
- Neuroinformatics
- Brain atlases
- Brain anatomy
Courses taught
- IMB9345 – Neuroscience data integration through use of digital brain atlases
Background
- PhD Neuroscience, University of Oslo, Norway
- MSc Neuroscience, Norwegian University of Science and Technology, Norway
Awards
Publications
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Bjerke, Ingvild Elise; Yates, Sharon Christine; Carey, Harry; Bjaalie, Jan G. & Leergaard, Trygve B.
(2023).
Scaling up cell-counting efforts in neuroscience through semi-automated methods.
iScience.
ISSN 2589-0042.
26(9).
doi:
10.1016/j.isci.2023.107562.
Full text in Research Archive
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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
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Bjerke, Ingvild Elise; Yates, Sharon Christine; Laja, Arthur; Witter, Menno; Puchades, Maja & Bjaalie, Jan G.
[Show all 7 contributors for this article]
(2020).
Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain.
iScience.
ISSN 2589-0042.
24:101906(1),
p. 1–52.
doi:
10.1016/j.isci.2020.101906.
Full text in Research Archive
Show summary
The calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Information about the numbers of these neurons across brain regions is required to understand their functional roles but is scarcely available. Employing semi-automated image analysis, we performed brain-wide analysis of immunohistochemically stained parvalbumin and calbindin sections and show that these neurons distribute in complementary patterns across the mouse brain. Parvalbumin neurons dominate in areas related to sensorimotor processing and navigation, whereas calbindin neurons prevail in regions reflecting behavioral states. We also find that parvalbumin neurons distribute according to similar principles in the hippocampal region of the rat and mouse brain. We validated our results against manual counts and evaluated variability of results among researchers. Comparison of our results to previous reports showed that neuron numbers vary, whereas patterns of relative densities and numbers are consistent.
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View all works in Cristin
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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.
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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.
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Puchades, Maja Amedjkouh; Yates, Sharon Christine; Bjerke, Ingvild Elise & Carey, Harry
(2023).
Rodent atlasing tools and the QUINT workflow.
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Leergaard, Trygve B.; Bjerke, Ingvild Elise; Bjaalie, Jan G.; Palomero-Gallagher, Nicola; Puchades, Maja & Carey, Harry
[Show all 7 contributors for this article]
(2022).
Neuroscience data integration through use of digital brain atlases .
Show summary
This two-day course will provide a hands-on introduction to three-dimensional reference atlases for the rat and mouse brain, and demonstrate how such atlases can be utilized to integrate and analyze heterogeneous neuroscience data. Students will gain updated knowledge about current approaches to assigning anatomical location to experimental data from the brain, and acquire basic skills in associated analytic tools. Invited speaker Nicola Palomero-Gallagher will give a lecture on neuroanatomy. Jan Bjaalie, Trygve Leergaard and co-workers Camilla Blixhavn, Ingvild Bjerke, Maja Puchades, Sharon Yates and Harry Carey from the Neural Systems Laboratory (University of Oslo) will introduce new concepts for data integration and development of murine brain atlas resources established in context of the European Human Brain Project.
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Bjerke, Ingvild Elise; Imad, Jala; Clascá, Francisco; Groenewegen, Henk J.; Bjaalie, Jan G. & Leergaard, Trygve Brauns
(2022).
Waxholm Space atlas of the Sprague Dawley rat brain version 4: A volumetric atlas enabling data integration and analysis.
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Bjerke, Ingvild Elise
(2022).
Mouse and rat brain atlases: Registering and analysing rodent brain data
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Bjerke, Ingvild Elise; Leergaard, Trygve B.; Bjaalie, Jan G. & Kim, Jee Hyun
(2022).
Quantitative map of dopamine 1- and 2-receptor positive cells in the developing mouse forebrain.
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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.
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Bjerke, Ingvild Elise; Cullity, Ellen Rose; Kjelsberg, Kasper; Charan, Kristel; Leergaard, Trygve B. & Kim, Jee Hyun
(2022).
Map of dopamine 1- and 2-receptor positive cells in the developing mouse forebrain.
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Leergaard, Trygve B.; Bjerke, Ingvild Elise; Palomero-Gallagher, Nicola; Witter, Menno; Dickscheid, Timo & Puchades, Maja
[Show all 7 contributors for this article]
(2021).
Neuroscience data integration through use of digital brain atlases.
Show summary
Kurs om data integrasjon og digitale hjerne atlas.
September 1:
INTRODUCTION (Trygve Leergaard & Ingvild Bjerke)
SESSION 1: Concepts for sharing and integration of neuroscience data (Jan Bjaalie)
SHORT BREAK
SESSION 2: Navigating the brain (Nicola Palomero-Gallagher, Menno P. Witter, Timo Dickscheid)
LUNCH BREAK
SESSION 2: continued
SHORT BREAK
SESSION 3: Introduction to EBRAINS digital brain atlas resources (Timo Dickscheid & Maja Puchades)
CLOSURE DAY 1
September 2:
SESSION 4: Sharing and assigning location parameters to murine data (Ingvild Bjerke & Maja Puchades)
SHORT BREAK
SESSION 4, continued
SHORT BREAK
SESSION 5: Automated quantification of experimental murine image data (Sharon Yates & Maja Puchades)
LUNCH BREAK
SESSION 5, continued (Sharon Yates)
BREAK
SESSION 6: Visions of data integration in the future (Jan Bjaalie)
CLOSURE DAY 2: Evaluation and preparation for exam task (Trygve Leergaard)
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Puchades, Maja ; Yates, Sharon Christine; Bjerke, Ingvild Elise; Groeneboom, Nicolaas; Csucs, Gergely & Leergaard, Trygve B.
[Show all 7 contributors for this article]
(2021).
Implementing the QUINT workflow for spatial quantitative analysis of labelling in mice and rats.
Show summary
Research in small animal disease models and simulation depend on quantitative comparisons of cellular and molecular measures in large groups of specimens, requiring efficient and reproducible methods.
The EBRAINS QUINT workflow combines 3D atlas registration tools (QuickNII and VisuAlign) with machine learning based image segmentation (ilastik), and a tool for quantitative analysis on whole brain and regional level (Nutil Quantifier).
Workflow descriptions, video tutorials, courses and email sup
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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.
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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.
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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.
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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.
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Bjerke, Ingvild Elise; Øvsthus, Martin; Andersson, Krister Andreas; Bjaalie, Jan G. & Leergaard, Trygve B.
(2018).
Best practices for determining and documenting neuroanatomical locations in the rodent brain.
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Øvsthus, Martin; Bjerke, Ingvild Elise; Yates, Sharon Christine; Bjaalie, Jan G. & Leergaard, Trygve Brauns
(2018).
Mapping topographical organization in mouse brain subcortical axonal projections using Human Brain Project infrastructure.
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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.
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Leprince, Y; Coello, Sebastian Christopher; Csúcs, Gergely; Chervakov, P; Darine, Dmitri Aleksandrovitsj & Øvsthus, Martin
[Show all 12 contributors for this article]
(2017).
Interactive tools for registering of 2D and 3D images to reference atlases.
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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.
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Bjerke, Ingvild Elise; Andersson, Krister Andreas; Øvsthus, Martin; Puchades, Maja ; Bjaalie, Jan G. & Leergaard, Trygve B.
(2017).
Navigating the rodent brain: Best practice recommendations for determining and documenting spatial location for neuroscience data .
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Andersson, Krister; Øvsthus, Martin; Bjerke, Ingvild Elise; Puchades, Maja ; Telefont, Martin & Jeff, Muller
[Show all 9 contributors for this article]
(2017).
Data integration through digital brain atlasing: Human Brain Project infrastructure.
Show summary
The Human Brain Project is building an ICT-based scientific research infrastructure that will permit researchers to advance our knowledge in the fields of neuroscience through data exploration, analytics and simulation at multiple levels of brain organization. Experimental neuroscience is connected to the infrastructure through systems for organizing and managing heterogeneous research data. These data systems are initially tested by data producing laboratories in the HBP, and will ultimately be opened for the community. HBP data curation services support users in elevating the level of data consistency and in the migration of data to the open domain. The starting point for research projects that will use HBP resources is the HBP Collaboratory, a rich collaborative workspace which is open to the community. The Collaboratory provides guidance and access to resources, including storage for data and a workbench for entering and organizing metadata. As a central element, the Collaboratory provides high-quality reference atlases of the rodent and human brain, together with appropriate tools and workflows that allow users to register data to the atlases for their study, and to perform initial analysis of data. It also links to important external data repositories and services. Here we present an overview of currently available reference atlases, tools and workflows. We exemplify the use of these resources in a range of neuroscience projects, ranging from brain-wide mapping of molecular level information to identification of precise location of electrophysiology recording sites. With coordinates corresponding to reference atlas space, harvested through the workflow, valuable metadata for future search and analysis of data are captured. Furthermore, with data aligned to reference atlases, analysis of the spatial distribution of events, labeled elements, and regions of interest in image material is strongly supported. Following registration to reference atlas, subsequent image processing and analysis steps delivers lists of extracted features corresponding to atlas structures, enabling quantitative regional analysis. We exemplify analytical workflows producing automated quantification and spatial analysis of labeling in series of histological section images from whole rodent brain. These and other atlas related workflows will be made available as HBP software services.
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Bjerke, Ingvild Elise; Andersson, Krister; Øvsthus, Martin; Puchades, Maja ; Bjaalie, Jan G. & Leergaard, Trygve Brauns
(2017).
Determining and documenting the anatomical location of experimental neuroscience data: Best practice recommendations.
Show summary
Anatomical location is a key parameter for interpretation and comparison of neuroscientific data. Location is typically determined by looking up diagrams in anatomical reference atlases, communicated using anatomical terms, and shown in representative images. But the documentation provided varies considerably among scientific publications. Essential information about nomenclature and reference atlases, or criteria used to define boundaries of structures is often missing. This lack of accuracy limits the opportunities for comparing and integrating data from different publications, and could lead to failure in replicating scientific experiments. To clarify and address this challenge, we have investigated current practice for assigning and documenting anatomical location for different categories of experimental neuroscience data reported in > 120 articles investigating the rodent brain. Our findings show that the specificity and accuracy of anatomical documentation in most cases can be considerably improved with relatively simple procedures. We here suggest some general and method-specific recommendations for such improvements, and discuss how these steps may contribute to increase the accuracy of anatomical descriptions and data interpretation. We demonstrate how new three-dimensional rodent brain reference atlases, and associated software tools for spatial registration of brain image data to a common anatomical space, offer new opportunities for efficient integration and comparison of neuroscience data.
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Puchades, Maja ; Csúcs, Gergely; Checinska, Martyna; Øvsthus, Martin; Bjerke, Ingvild Elise & Andersson, Krister
[Show all 8 contributors for this article]
(2017).
Neuroinformatics tool and workflow for anchoring of serial histological images in rodent brain 3D space.
Show summary
Reference atlases of the brain are important tools for assigning location to data captured in neuroscience experiments. Spatial alignment of sectional images to reference atlases is, however, challenging to perform for several reasons. Manual approaches applied to large series of sectional images are time consuming and, moreover, histological sections are often cut at angles deviating from the principal anatomical planes presented in conventional reference atlases. Novel 3D reference atlases and accompanying tools provide new opportunities for rapid and accurate spatial registration and integration of data in common atlas space. We here present QuickNII which is new tools for use with the Waxholm Space atlas for the rat brain and the Allen Mouse brain atlas for the mouse brain, and a workflow that allows users to 1) interactively generate customized atlas images (slices of the 3D reference atlas) corresponding to the plane of sectioning of any experimental image series, 2) superimpose atlas images onto experimental images using affine transformations to match key anatomical landmarks, 3) propagate the transformations across a series of images, 4) assign spatial reference atlas coordinates to the experimental images, and 5) allow viewing and analysis of the experimental data integrated in the reference atlas. We exemplify the workflow and use of our methods with a range of experimental data from neuroanatomical and neurophysiological investigations.
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Puchades, Maja ; Øvsthus, Martin; Bjerke, Ingvild Elise; Andersson, Krister; Csúcs, Gergely & Leergaard, Trygve Brauns
[Show all 7 contributors for this article]
(2017).
Data integration through digital brain atlasing: semiautomatic spatial registration of serial histological images to rodent brain 3D reference atlases.
Show summary
Reference atlases of the brain are important tools for assigning location to data captured in neuroscience experiments. Spatial alignment of sectional images to reference atlases is, however, challenging to perform for several reasons. Manual approaches applied to large series of sectional images are time consuming and, moreover, histological sections are often cut at angles deviating from the principal anatomical planes presented in conventional reference atlases. Novel 3D reference atlases and accompanying tools provide new opportunities for rapid and accurate spatial registration and integration of data in common atlas space. We here present new tools for use with the Waxholm Space atlas for the rat brain and the Allen Mouse brain atlas, and workflow that allows users to 1) interactively generate customized atlas images (slices of the 3D reference atlas) corresponding to the plane of sectioning of any experimental image series, 2) superimpose atlas images onto experimental images using affine transformations to match key anatomical landmarks, 3) propagate the transformations across a series of images, 4) assign spatial reference atlas coordinates to the experimental images, and 5) allow viewing and analysis of the experimental data integrated in the reference atlas. We exemplify the work flow and use of our methods with a range of experimental data from neuroanatomical and neurophysiological investigations.
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Puchades, Maja ; Bjerke, Ingvild Elise; Øvsthus, Martin; Andersson, Krister; Csúcs, Gergely & Leergaard, Trygve Brauns
[Show all 7 contributors for this article]
(2016).
Spatial registration of serial histological image data to reference brain atlases.
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Berggaard, Nina; Bjerke, Ingvild Elise; Paulsen, Anna Elisabeth Bråthen & Van der Want, Johannes
(2016).
Parvalbumin interneurons within a spatially modulating network: development and connectivity.
View all works in Cristin
Published
June 2, 2022 8:48 AM
- Last modified
June 2, 2022 8:48 AM
