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Neural Systems

NeSys is a computational neuroanatomy, neuroimaging, and neuroinformatics laboratory.

NeSys group photo

Photo: Carina Knudsen, Institute for Basic Medical Sciences, UiO

Research Interest 

Our laboratory performs histological studies in rodent models to characterise neuroanatomy, neural connections and brain diseases. We develop data sharing systems, brain atlases and tools for analysing brain architecture data. The group has a leading role in the development and operation of the EBRAINS research infrastructure.

Data sharing service

In collaboration with our EBRAINS partners, we contribute to the development of a data sharing platform for neuroscience, the EBRAINS Data and Knowledge services. We coordinate the EBRAINS curation service, which aims to make data discoverable and reusable through the platform.

Brain atlases

We develop and maintain open access, three-dimensional brain atlases in collaboration with anatomy experts. This includes the Waxholm Space atlas of the Sprague Dawley rat and developmental mouse brain atlases. The Waxholm Space atlas is the most comprehensive 3D rat brain atlas available and is still being developed to offer new and refined delineations. It is the anatomical framework for integrating rat brain data in EBRAINS and is available through the EBRAINS atlas services.

Software Tools

We develop neuroinformatics tools for analysing brain histology with a focus on small animal models. Our tools can be used to register serial section images to a reference brain atlas, to characterise labelled features within a reference atlas space, and to visualise brain architecture. The tools are available as downloadable software and online through the EBRAINS atlas services. As our goal is to support open and reproducible science, all the tools are open-source, open-access, and developed in collaboration with the research community.

About the group

The Experimental Neuroanatomy division, headed by Professor Trygve B. Leergaard, maps histology and system level neural connections in rodent models. The division has responsibility for advancing developments of the Waxholm Space atlas of the rat brain.

The Neuroinformatics division, headed by Professor Jan Bjaalie, develops analytical tools using brain atlases and large scale infrastructure for sharing of data and tools. The division has a leading role in operation of the EBRAINS Data and Knowledge Services.

Key publications

  • Kleven H, Bjerke IE, Clascá F, Groenewegen HJ, Bjaalie JG, Leergaard TB. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods. 2023. doi: 10.1038/s41592-023-02034-3.
  • Carey H, Pegios M, Martin L, Saleeba C, Turner AJ, Everett NA, Bjerke IE, Puchades MA, Bjaalie JG, McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. Nat Commun. 2023. doi: 10.1038/s41467-023-41645-4.
  • Kleven H, Gillespie T, Zehl L, Dickscheid T, Bjaalie T, Martone M, Leergaard T. AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Scientific Data. 2023. doi: 10.1038/s41597-023-02389-4
  • Leergaard TB, Bjaalie JG. Atlas-based data integration for mapping the connections and architecture of the brain. Science. 2022. doi: 10.1126/science.abq2594.
  • Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU, Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front Neuroinform. 2019. doi: 10.3389/fninf.2019.00075.

Full publication list

Our research is funded by

European Union's Horizon 2020 Framework Programme for Research and Innovation

  • EBRAINS Prep
  • EBRAINS Health
  • SciLake
  • EBRAINS 2.0

The Research Council of Norway

  • INCF Norwegian Node

The University of Oslo

  • NORBRAIN
  • SHAREbrain

UNIFOR Frimed

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Published Feb. 21, 2011 3:37 PM - Last modified Mar. 15, 2024 2:14 PM

Contact

Dept. of Molecular Medicine
Domus Medica
Gaustad
Sognsvannsveien 9
0372 Oslo

Group leaders

Participants

Detailed list of participants