Abstract
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.
Highlights
Our senses of hearing and balance are secured by the sensory cells of the inner ear, the hair cells, which transform the mechanical stimuli of sound or head movement into electrical signals our brain can understand through a process called mechanoelectrical transduction (MET)
A list of proteins were shown to be important for the hair cell stereocilia bundle structure and function, many of which were localized to the bundle using variations of immunogold labeling protocols, and observed with electron microscopy (EM) techniques, mostly using transmission electron microscopy (TEM)[2,3,4,5,6,7,8,9,10,11,12,13,14,15] and more lately using scanning electron microscopy (SEM)[16,17,18,19,20,21]
In the most recent years though, serial electron microscopy techniques have become more accessible for use in biology, mounting a new body of work using 3D EM approaches[17,22,23]
Summary
Our senses of hearing and balance are secured by the sensory cells of the inner ear, the hair cells, which transform the mechanical stimuli of sound or head movement into electrical signals our brain can understand through a process called mechanoelectrical transduction (MET). Movies illustrating 3D localization of PKHD1L1 in immunogold labeled outer hair cell stereocilia bundles using FIB‐ SEM (postnatal day 4) in a single OHC, and 3D cumulative distribution map of anti‐PKHD1L1 immuno‐gold beads from six mouse OHC stereocilia bundles (postnatal day 4) were deposited at figshare[27] Both movies are published with permission from the original study[17]. While describing the details of the MATLAB script, designed to work with any tower-shaped object (cilia or not), we refer to these structures as ‘towers’
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