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Workflow for mapping tracer injection studies of the common marmoset into a reference template

Piotr Majka1, 2*, Tristan A. Chaplin1, 3, 4, Hsin-Hao Yu1, 3, Vadim Pinskiy5, Partha Mitra5, Daniel K. Wójcik2 and Marcello Rosa1, 3, 4
  • 1 Monash University, Department of Physiology, Australia
  • 2 Nencki Institute of Experimental Biology, Poland
  • 3 Australian Research Council Centre of Excellence for Integrative Brain Function, Australia
  • 4 Monash Vision Group, Monash University, Australia
  • 5 Cold Spring Harbor Laboratories, United States

Tracer injection studies provide a valuable insight into brain connectivity. However, the two dimensional nature of such data renders it difficult to make comparisons between injections performed in different animals or between tracer injection studies and those conducted with inherently three dimensional methods like resting state functional magnetic resonance or diffusion tensor imaging. In order to facilitate such comparisons, one has to bring the two dimensional data into a common, three dimensional space. In this study we propose and validate an automated workflow for mapping the common marmoset connectivity data obtained from tracer injection studies into reference template space of a stereotaxic atlas [1, 2]. Nine marmosets were injected with fluorescent retrograde tracers in the dorsolateral prefrontal cortex. These tracers label the cell bodies of neurons that send projections to the injection site, thus providing a map of neuronal inputs. Due to the limited number of distinguishable tracers, building a map of connectivity requires the registration of multiple specimens to a common atlas. The process of mapping data obtained from a single specimen into the atlas space comprises several steps. In the initial stage, the location of stained cells marked on the fluorescence sections are aligned with the neighboring Nissl sections. Afterwards, the Nissl stained sections are stacked and reconstructed into volumetric form. The reconstruction is initially performed with affine transformations followed by deformable warping. The latter step removes section specific distortions and allows for more reliable subsequent deformable mapping [3] into the atlas space. The process yields a set of transformations which are then applied to the actual cells locations. In the final step the individual cells are assigned to a particular brain structure based on the atlas parcellation. The described process was conducted for nine test cases and resulted in a database of the cell's coordinates in the atlas space. The results can be visualized on a 3D model of the marmoset brain or projected onto a cortical flat maps. The reliability of the workflow was assessed in two ways. First, by comparing the number of the cells in each cortical area indicated by the automated approach with the count determined manually by an anatomist. Second, by measuring distances between mapping-based and ground truth locations of the injection sites. The established workflow allows the processing of the additional cases to produce a spatially defined connectivity map of the marmoset cortex, independent of anatomical parcellation scheme [4], unlike the traditional method relying on prior assignment of data to discrete anatomical structures. Additionally, it allows purely spatially based comparisons of connectivity with three dimensional imaging methods.

References


[1] Paxinos, G., Watson, C., Petrides, M., Rosa, M., & Tokuno, H. (2011). The Marmoset Brain in Stereotaxic Coordinates (1st ed.). Academic Press.

[2] Chaplin TA, Yu H, Majka P, Yen CC, Bakola S, Kowalski JM, Hung C, Burman KJ, Wójcik DK, Silva AC and Rosa MG (2013). Mapping the marmoset monkey cortex and the construction of a multimodal digital atlas. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00122

[3] Avants, B. B., Tustison, N. J., Song, G., Cook, P. a, Klein, A., & Gee, J. C. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. NeuroImage, 54(3), 2033–44. doi:10.1016/j.neuroimage.2010.09.025

[4] Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A. M., et al. (2014). A mesoscale connectome of the mouse brain. Nature. doi: 10.1038/nature13186

Keywords: marmoset, Cerebral Cortex, evolution, MRI, connectome, cortical mapping, atlasing

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Poster, not to be considered for oral presentation

Topic: Digital atlasing

Citation: Majka P, Chaplin TA, Yu H, Pinskiy V, Mitra P, Wójcik DK and Rosa M (2015). Workflow for mapping tracer injection studies of the common marmoset into a reference template. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00022

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Received: 06 Apr 2015; Published Online: 05 Aug 2015.

* Correspondence: Dr. Piotr Majka, Monash University, Department of Physiology, Melbourne, VIC, Australia, p.majka@nencki.edu.pl