Event Abstract

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

  • 1 Nencki Institute of Experimental Biology, Poland
  • 2 Department of Physiology, Monash University, Australia
  • 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

The goal of the study is to establish an automated workflow for mapping 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. Retrograde 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. Furthermore, registration to a common coordinate system will allow purely spatially based comparisons of connectivity unlike the traditional method relying on prior assignment of data to discrete anatomical structures.

Several steps are required to map the data obtained from a single specimen into the atlas space. During the initial stage, the locations of stained cells marked on the fluorescence sections are transferred to 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 will be conducted for nine test cases and will result in a database of the cell's coordinates in the atlas space.

The reliability of the workflow will be assessed by comparing the number of the cells in each cortical area indicated by the automated approach with the count determined manually by an anatomist. Once established, the workflow will allow the processing of the remaining cases to produce a spatially defined connectivity map of the marmoset cortex, independent of anatomical parcellation scheme [4]. Furthermore, this map can be used as a gold standard in DTI validation studies.


[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 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.

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

Topic: Digital atlasing

Citation: Majka P, Chaplin TA, Yu H, Pinskiy V, Mitra P, Rosa M and Wójcik DK (2014). Automated workflow for mapping tracer injection studies of the common marmoset into a reference template. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00038

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Received: 04 Apr 2014; Published Online: 04 Jun 2014.

* Correspondence: Mr. Piotr Majka, Nencki Institute of Experimental Biology, Warsaw, Poland, p.majka@nencki.edu.pl