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Multi-level atlas of the rodent brain: data integration and quantitative analysis
Norway (NMSA) - University of Oslo, Oslo
Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo. Visiting address: Domus Medica, Gaustad, Sognsvannsveien 9, 0372 Oslo
Trygve B. Leergaard
Type of Research Project
- Basic science
What is the background of the project?
Experimental neuroscience research projects typically involve analysis of cellular markers observed in histological sections from mouse or rat brains. Analysis of such data requires careful assignment of anatomical location and quantification of labeling in regions of interest. Improved digital camera technology, robotic microscopes, and computational hardware now allow high-throughput acquisition of high-resolution ‘virtual microscopy’ images covering very large tissue areas. Anatomical evaluation of microscopic images is greatly facilitated by spatial registration to 3-D anatomical reference atlases. The student project will contribute to one of several ongoing neuroanatomical and neuroinformatics related activities delivering tools, IFMSA International Secretariat, c/o IMCC, Nørre Allé 14, 2200 København N., Denmark workflows, and data to the EU Human Brain Project. These activities include development of 3D reference atlas resources for rodent brains, spatial integration and automated analysis of experimental image data, with the overall objective of sharing open data in accordance with the FAIR guidlines stating that data should be Findable, Accessible, Interoperable and Reusable.
What is the aim of the project?
To contribute to proof-of-concepts demonstrations of how heterogeneous experimental neuroanatomical data can be integrated and utilized to generate quantitative data from regions of interest.
What techniques and methods are used?
We will use novel neuroinformatics tools and workflows developed in the host laboratory to register serial microscopic image data from rodent brains to a common spatial template, assign spatial coordinates, and perform focused strategic analyses in selected regions-of-interest to extract qualitative and quantitative morphological data.
What is the role of the student?
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- The tasks of the student will be performed on his/her own
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
Students will participate in well-defined small sub- projects where they will manage and spatially register series of high-resolution microscopic images to spatial templates, and perform a limited number of morphological analyses which will yield strategically important quantitative data that are defined within 3-D atlas space. Students will be trained in the use of tools for spatially aligning serial rodent brain section images with 3-D reference atlases, and extracting and quantifying labeled features observed in regions of interest. The work will be carried out independently as well as in teams.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
Yes, tutorials and workflow descriptions will be provided, and hands-on training will be given.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a presentation
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
General knowledge and understanding of neuroanatomy and histology. Ability to make observations, writing reports, and to learn and apply different computer software tools.
Are there any legal limitations in the student’s involvement
Type of students accepted
This project accepts: - Medical students - Graduated students (less than 6 months) - Students in biomedical fields
- Papp et al.; Neuroimage 97:374-386; 2014
- Lillehaug et al.; Neurobiol Aging 35:556-564; 2014
- Lillehaug et al.; Sci Data; 6:190028; 2019
- Zakiewicz et al.; PLoS One; 6(8):e22669; 2011
- Puchades et al.; PLoS One; 14(5):e0216796; 2019
- Osen et al.; Neuroimage 199:38-56; 2019
- Bjerke et al.; Front Neuroanat; 12:82; 2019
- https://ebrains.eu/ and http://rbwb.org/
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