Neuroanatomical Imaging

neuroanatomical imaging

Image courtesy of Sebastian Seung

Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices—or “sections”—and imaging them, however, handling 100-106 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e.,102-103 sections. Our lab is developing a tissue section handling device that transports and positions sections accurately and repeatably for automated, robotic section pick-up and placement onto an imaging substrate.

Selected Publications

T. Lee, Batch processing of brain tissue sections for millimeter-scale serial section transmission electron microscopy connectomics, Doctoral Dissertation, Summer 2019


Timothy J. Lee, Mighten C. Yip, Aditi Kumar, Colby F. Lewallen, Daniel J. Bumbarger, R. Clay Reid and Craig R. Forest, Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics, eNeuro 24 February 2020, 7 (2) ENEURO.0328-19.2019; DOI:


T.J. Lee, A. Kumar, A.H. Balwani, D. Brittain, S. Kinn, C.A. Tovey, E.L. Dyer, N.M. da Costa, R.C. Reid, C.R. Forest*, D.J. Bumbarger* (*co-corresponding authors). Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation, PLOS One 13(10): e0206172. (2018)


T.J. Lee, C.F. Lewallen, D.J. Bumbarger, P.J. Yunker, R.C. Reid, C.R. Forest. Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions, Journal of Colloid and Interface Science (2018). DOI: 10.1016/j.jcis.2018.07.068


J. Lee, I. Kolb, C.R. Forest, C.J. Rozell, Cell membrane tracking in living brain tissue using differential interference contrast microscopy, IEEE Transactions on image processing, 2018 Apr; 27(4):1847-1861. doi: 10.1109/TIP.2017.2787625.

A.S. Chuong, M.L. Miri, L.C. Acker, S.B. Kodandaramaiah, M.A. Henninger, M. Ogawa, R.C. Bandler, N.C. Klapoetke, X. Gu, B.D. Allen, C.R. Forest, B.Y. Chow, X. Han, J.A. Cardin, E.S. Boyden, Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience. Vol 17, p. 1123-1129, July 2014.