Quantifying cellular parameters across the murine brain: New practices for integrating and analysing neuroscience data using 3D brain atlases
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AbstractEfforts to advance our understanding of the brain has led to an exponentially growing number of publications. However, research reporting practices are often insufficient for independent researchers to interpret and replicate findings, and underlying data are rarely made available. This hampers efforts to compare, integrate and re-use data from different studies. Bjerke and colleagues aimed to develop new standards and workflows to facilitate data integration in neuroscience. They defined new standards for reporting anatomical locations in the murine brains, and showed how new methods to spatially define data in three-dimensional brain reference atlases can facilitate integration of data from multiple studies. They further built a database of published quantitative data from the murine basal ganglia, demonstrating how such data can be collected and compared. Lastly, they combined spatial registration of microscopic images to brain atlases with semi-automatic image analysis to quantify cell numbers and densities across murine brains. The work presented in this thesis together demonstrates how neuroscience data can be organized, integrated, and shared to facilitate their re-use.
List of papers
|Paper I: Bjerke IE, Øvsthus M, Andersson KA, Blixhavn CH, Kleven H, Yates SC, Puchades MA, Bjaalie JG & Leergaard TB. Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies. Frontiers in Neuroanatomy 12 (2018) DOI: 10.3389/fnana.2018.00082. The article is included in the thesis. Also available at: https://doi.org/10.3389/fnana.2018.00082|
|Paper II: Bjerke IE, Puchades M, Bjaalie JG & Leergaard TB. Database of literature derived cellular measurements from the murine basal ganglia. Scientific Data (2020) DOI: 10.1038/s41597-020-0550-3. The article is included in the thesis. Also available at: https://doi.org/10.1038/s41597-020-0550-3|
|Paper II: Bjerke IE, Yates SC, Laja A, Witter MP, Puchades M, Bjaalie JG & Leergaard TB. Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain: Complementary patterns and cross-species comparison. Manuscript. Oublished in iScience. 2021, 24 (1):101906, DOI: 10.1016/j.isci.2020.101906. The article is included in the thesis. Also available at: https://doi.org/10.1016/j.isci.2020.101906|