Scaling Up 3D Imaging, Analysis, and Culture of Complex Brain Models

"Pascal meditated upon outer space, but we need only turn our thoughts inward to feel his dread. Inside every one of our skulls lies an organ so vast in its complexity that it might as well be infinite."

― Sebastian Seung, Connectome: How the Brain's Wiring Makes Us Who We Are

This thesis summarizes a body of work in scaling up experimental techniques used in neuroscience research. Specifically, this thesis describes technological advances that facilitate large-scale 3D imaging, analysis, and culture of complex brain models.

A PDF version of the thesis is available here

Justin Swaney, PhD Candidate
Department of Chemical Engineering
Massachusetts Institute of Technology
[email protected]

Publications

E. Murray*, J. H. Cho*, D. Goodwin*, T. Ku*, J. Swaney*, S. Y. Kim,H. Choi, Y. G. Park, J. Y. Park, A. Hubbert, M. McCue, S. Vassallo, N. Bakh, M. P. Frosch, V. J. Wedeeng, H. S. Seung, K. Chung†. "Simple, scalable proteomic imaging for high-dimensional profiling of intact systems", Cell, 2015, 163, 6, 1500–1514

T. Ku*, J. Swaney*, J. Y. Park*, A. Albanese, E. Murray, J. H. Cho, Y. G. Park, V. Mangena, J. Chen, K. Chung†. "Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues", Nature Biotechnology, 2016, doi:10.1038/nbt.3641.

J. Swaney*, L. Kamentsky*, N. B Evans, K. Xie, Y. G. Park, G. Drummond, D. H. Yun, K. Chung†. "Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy", bioRxiv, 2019, DOI:10.1101/576595

D. H. Yun*, Y. G. Park*, J. H. Cho*, L. Kamentsky, N. B. Evans, A. Albanese, K. Xie, J. Swaney, C. H. Sohn, Y. Tian, Q. Zhang, G. Drummond, W. Guan, N. DiNapoli, H. Choi, H. Y. Jung, L. Ruelas, G. Feng, K. Chung†. "Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping", bioRxiv, 2019, DOI:10.1101/660373

A. Albanese*, J. Swaney*, D. H. Yun, N. Evans, J. Antonucci-Johnson, V. Pham, C. Delepine, M. Sur, L. Gehrke, K. Chung†2. “3D imaging and high content morphological analysis of intact human cerebral organoids”, Cell (in preparation), 2019.

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References

This thesis was based on the following template:

Tom Pollard et al. (2016). Template for writing a PhD thesis in Markdown. Zenodo. http://dx.doi.org/10.5281/zenodo.58490