Reconstruction of Serial Sections

Serial sections The principle of using serial sections to build-up a reconstruction of biological tissue has been around a long time. However, it suffers from many drawbacks. Apart from the simple problem that it takes a long time to cut hundreds of sections, mount them on slides, stain them, photograph them and then process them through a computer (while trying not to loose any of them), there is also a theoretical difficulty in knowing how to fir them back together within the 3-D reconstruction. One common approach is simply too match up the structures on adjacent sections with each other. This will always suffer from the problem that structures will tend to become straightened-out along the axis perpendicular to the sections. This is illustrated by an exaggerated example in the following figure.

A tubular structure is embedded in a block (left) and then cut into sections (middle). In many commonly-used techniques, such as embedding the tissue in parafin wax, the embedding material is washed/dissolved away from the tissue once the sections are mounted onto glass slides. The only information available for aligning the sections is the tissue itself. However, in this case, information about the curvature of the tube has been lost, so aligning the sections to each other results in a straightened tube.

One solution to this problem is to use thick sections which retain some 3-D information about the orientation of structures which pass through the section. Thick sections like these can be scanned using a confocal microscope, and reconstructed as shown below.

In the case of thick sections the true shape of the structures can be reconstructed by aligning the bottom of one thick section with the top of the next one (see confocal).

An alternative solution which uses thin sections is to provide external registration markers. In one technique (Streicher et al., 2000) the specimen is embedded in a resin block which is not dissolved away after the sections have been mounted. Before sectioning, vertical holes are drilled into the block around the specimen. These holes can be seen adjacent to the tissue in the mounted sections, so that a reconstruction based on these, rather than on the tissue itself, will retain its true 3-D shape.

A reconstruction scheme which uses external markers. Before sectioning, vertical holes are drilled into the block (red bars) around the specimen. After sectioning these holes indicate how the sections should be aligned.

A reconstruction of the Scgn10 gene in a TS17 mouse embryo using the block-drilling technique (courtesy of Streicher, 2000). This is from the geneEMAC database of gene expression hosted in Vienna.