X-ray micro-computed tomography of postmortem brain tissue using potassium dichromate as a contrast agent.

No abstract available.

Microscopic dual-energy CT (microDECT): a flexible tool for multichannel ex vivo 3D imaging of biological specimens.

Dual-energy computed tomography (DECT) uses two different x-ray energy spectra in order to differentiate between tissues, materials or elements in a single sample or patient. DECT is becoming increasingly popular in clinical imaging and preclinical in vivo imaging of small animal models, but there have been only very few reports on ex vivo DECT of biological samples at microscopic resolutions. The present study has three main aims. First, we explore the potential of microscopic DECT (microDECT) for delivering isotropic multichannel 3D images of fixed biological samples with standard commercial laboratory-based microCT setups at spatial resolutions reaching below 10 µm. Second, we aim for retaining the maximum image resolution and quality during the material decomposition. Third, we want to test the suitability for microDECT imaging of different contrast agents currently used for ex vivo staining of biological samples. To address these aims, we used microCT scans of four different samples stained with x-ray dense contrast agents. MicroDECT scans were acquired with five different commercial microCT scanners from four companies. We present a detailed description of the microDECT workflow, including sample preparation, image acquisition, image processing and postreconstruction material decomposition, which may serve as practical guide for applying microDECT. The MATLAB script (The Mathworks Inc., Natick, MA, USA) used for material decomposition (including a graphical user interface) is provided as a supplement to this paper (https://github.com/microDECT/DECTDec). In general, the presented microDECT workflow yielded satisfactory results for all tested specimens. Original scan resolutions have been mostly retained in the separate material fractions after basis material decomposition. In addition to decomposition of mineralized tissues (inherent sample contrast) and stained soft tissues, we present a case of double labelling of different soft tissues with subsequent material decomposition. We conclude that, in contrast to in vivo DECT examinations, small ex vivo specimens offer some clear advantages regarding technical parameters of the microCT setup and the use of contrast agents. These include a higher flexibility in source peak voltages and x-ray filters, a lower degree of beam hardening due to small sample size, the lack of restriction to nontoxic contrast agents and the lack of a limit in exposure time and radiation dose. We argue that microDECT, because of its flexibility combined with already established contrast agents and the vast number of currently unexploited stains, will in future represent an important technique for various applications in biological research.

Zebrafish in context: uses of a laboratory model in comparative studies.

With the recent interest in the reintegration of evolutionary and developmental biology has come a growing need for understanding the phylogenetic relations and degree of generality of the model organisms upon which we rely so heavily. In vertebrate biology the zebrafish Danio rerio has become a paradigmatic system for studies at levels of organization from molecular to interspecific. Studies of model systems in development are often techniques-driven rather than questions-based; however, informative hypotheses for developmental research can be derived from phylogenetic distributions of characters. With some understanding of how general the characters of interest are, a thoughtful comparison of the requirements of the questions with the lists of available embryos, reagents, and protocols can guide choices of new vertebrate models. We describe here the phylogenetic placement of zebrafish within the vertebrate world and discuss how generally observations on zebrafish can be taken to apply. We outline a practical protocol for investigating development in a comparative context, illustrated with an example from an ongoing study of teleost tail fin evolution. The principles and procedures presented here apply equally well to any comparative study with an interest in evolution, at any level of phylogeny from intraspecific studies to comparisons across phyla.

Homeobox genes in axolotl lateral line placodes and neuromasts.

Gene expression has been studied in considerable detail in the developing vertebrate brain, neural crest, and some placode-derived organs. As a further investigation of vertebrate head morphogenesis, expression patterns of several homeobox-containing genes were examined using whole-mount in situ hybridization in a sensory system primitive for the vertebrate subphylum: the axolotl lateral lines and the placodes from which they develop. Axolotl Msx-2 and Dlx-3 are expressed in all of the lateral line placodes. Both genes are expressed throughout development of the lateral line system and their expression continues in the fully developed neuromasts. Expression within support cells is highly polarized. In contrast to most other observations of Msx genes in vertebrate organogenesis, expression of Msx-2 in developing lateral line organs is exclusively epithelial and is not associated with epithelial-mesenchymal interactions. A Hox-complex gene, Hoxb-3, is shown to be expressed in the embryonic hindbrain and in a lateral line placode at the same rostrocaudal level, but not in other placodes nor in mature lateral line organs. A Hox gene of a separate paralog group, Hoxa-4, is expressed in a more posterior hindbrain domain in the embryo, but is not expressed in the lateral line placode at that rostrocaudal level. These data provide the first test of the hypothesis that the neurogenic placodes develop in two rostrocaudal series aligned with the rhombomeric segments and patterned by combinations of Hox genes in parallel with the central nervous system.

Experimental considerations for 2-D acoustooptic spectrum analysis.

A 2-D acoustooptic spectrum analyzer with the associated reference function generator and real-time image processor has been constructed. The operation of the analyzer and the experimental considerations for obtaining a high resolution spectrum in real time are described.