Serial scanning electron microscopy of anti-PKHD1L1 immuno-gold labeled mouse hair cell stereocilia bundles

June 17, 2020

Maryna V. Ivanchenko (1), Marcelo Cicconet (2), Hoor Al Jandal (1,3), Xudong Wu (1), David P. Corey (1), Artur A. Indzhykulian (1,4)
Scientific Data, 7, Issue 182, June 2020: 182. DOI: 10.1038/s41597-020-0509-4


Serial electron microscopy techniques have proven to be a powerful tool in biology. Unfortunately, the data sets they generate lack robust and accurate automated segmentation algorithms. In this data descriptor publication, we introduce a serial focused ion beam scanning electron microscopy (FIB-SEM) dataset consisting of six outer hair cell (OHC) stereocilia bundles, and the supranuclear part of the hair cell bodies. Also presented are the manual segmentations of stereocilia bundles and the gold bead labeling of PKHD1L1, a coat protein of hair cell stereocilia important for hearing in mice. This depository includes all original data and several intermediate steps of the manual analysis, as well as the MATLAB algorithm used to generate a three-dimensional distribution map of gold labels. They serve as a reference dataset, and they enable reproduction of our analysis, evaluation and improvement of current methods of protein localization, and training of algorithms for accurate automated segmentation.

How Our Software Was Used

Dragonfly was used to perform image alignment, stereocilia and gold bead segmentation, and 3D reconstruction.

Author Affiliation

(1) Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA.
(2) Image and Data Analysis Core, Harvard Medical School, 43 Shattuck St, Boston, MA, 02115, USA.
(3) Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
(4) Department of Otolaryngology, Harvard Medical School and Massachusetts Eye and Ear, 243 Charles St, Boston, MA, 02114, USA.