Microscopic dual‐energy CT (microDECT): a flexible tool for multichannel ex vivo 3D imaging of biological specimens
Abstract
Summary: 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 m. 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.
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In laboratory micro-CT, image properties differ largely among specimens as staining levels and scanning conditions vary.
“in laboratory micro-CT, image properties differ largely among specimens as staining levels and scanning conditions vary 23”
From High-throughput phenomics of global ant biodiversity (2026) · cites this paper as [23]
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High-throughput phenomics of global ant biodiversity
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- Authors
- HANDSCHUH, S., BEISSER, C. J., RUTHENSTEINER, B., & METSCHER, B. D.
- Affiliations
- University of Vienna (AT)
- Bavarian State Collection of Zoology (DE)
- Corresponding author
- HANDSCHUH, S.
- Venue
- Journal of Microscopy
- Publisher
- Wiley
- Published
- 2017-03-07
- Volume
- 267
- Issue
- 1
- Pages
- 3-26
- ISSN
- 0022-2720 (ISSN-L)
- 1365-2818
- OpenAlex
- W2593229214
- Cited by
- 48
- References
- 97
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 4 · 2023: 1 · 2022: 9 · 2021: 9 · 2020: 7 · 2019: 5 · 2018: 5 · 2017: 1
- FWCI
- 2.21
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Microscopy (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Advanced X-ray and CT Imaging
- Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Medical Imaging Techniques and Applications
- Keywords
- dual-energy CT, micro-CT, ex vivo imaging, material decomposition, X-ray contrast agents, mineralized tissue, beam hardening
- MeSH terms
- Animals, Cats, Contrast Media, Fishes, Staining and Labeling, Imaging, Three-Dimensional, Mice, X-Ray Microtomography, Workflow
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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