Abstract
The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly—the equivalent of a petabyte of high resolution images each day. However, even high throughput image acquisition strategies generate images far more slowly (at present ~1 terabyte per day). We therefore developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections. Using WaferMapper, it is possible to map thousands of tissue sections at low resolution and target multiple points of interest for high resolution imaging based on anatomical landmarks. The program can also be used to expand previously imaged regions, acquire data under different imaging conditions, or re-image after additional tissue treatments.
Highlights
METHODSImaging automated tape-collecting ultramicrotome (ATUM) ultrathin section libraries with WaferMapper: a multi-scale approach to electron microscopy (EM) reconstruction of neural circuits
The three dimensional (3D) structure of biological tissues can be ascertained at high resolution by cutting plastic-embedded tissue into a series of ultrathin sections, imaging those sections with an electron microscope, and reconstructing the objects contained therein
Obtaining such volumetric reconstructions is especially useful for analysis of nervous system samples because nerve cells distribute their processes over extended volumes and only with the resolution of electron microscopy (EM) is it possible to identify the network of synaptic connections between all the neurons
Summary
Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits. Reviewed by: Julian Budd, University of Sussex, UK Richard J. The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly—the equivalent of a petabyte of high resolution images each day. We developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections.
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