Visualizing 3D Embryo and Tissue Morphology—A Decade of Using High-Resolution Episcopic Microscopy (HREM) in Biomedical Imaging, Volume II

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Biomedical Engineering and Materials".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 4505

Special Issue Editors


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Guest Editor
Division of Anatomy, Medical University of Vienna, Vienna, Austria
Interests: anatomy; episcopic 3D imaging; morphology; human; embryogenesis
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Division of Anatomy, Medical University of Vienna, Vienna, Austria
Interests: morphology; 3D imaging; cardiovascular morphogenesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

HREM is a digital volume data generation technique that offers near-histological detail in virtual 3D data of whole embryos of biomedical model organisms as well as small tissue samples. Introduced over 10 years ago, the HREM user community is steadily growing, and employs the method for phenotyping genetically engineered mouse embryos, biomedically challenged chick embryos and embryos of several other model organisms, as well as normal and pathological tissue samples of adult biomedical models and humans. Quite recently HREM also found its way into multimodal imaging pipelines, providing for the holistic visualization of normal and pathologic morphology and physiology of organisms at all levels of resolution. We invite authors to submit review articles focusing on applying HREM in various fields of biomedical research.

Prof. Dr. Wolfgang J. Weninger
Dr. Stefan H. Geyer
Guest Editors

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Keywords

  • episcopic imaging
  • phenotyping
  • bioimaging
  • high-resolution episcopic microscopy

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Published Papers (2 papers)

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Research

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24 pages, 5569 KiB  
Article
Timeline of Developmental Defects Generated upon Genetic Inhibition of the Retinoic Acid Receptor Signaling Pathway
by Marius Teletin, Manuel Mark, Olivia Wendling, Nadège Vernet, Betty Féret, Muriel Klopfenstein, Yann Herault and Norbert B. Ghyselinck
Biomedicines 2023, 11(1), 198; https://doi.org/10.3390/biomedicines11010198 - 12 Jan 2023
Cited by 4 | Viewed by 2082
Abstract
It has been established for almost 30 years that the retinoic acid receptor (RAR) signalling pathway plays essential roles in the morphogenesis of a large variety of organs and systems. Here, we used a temporally controlled genetic ablation procedure to precisely determine the [...] Read more.
It has been established for almost 30 years that the retinoic acid receptor (RAR) signalling pathway plays essential roles in the morphogenesis of a large variety of organs and systems. Here, we used a temporally controlled genetic ablation procedure to precisely determine the time windows requiring RAR functions. Our results indicate that from E8.5 to E9.5, RAR functions are critical for the axial rotation of the embryo, the appearance of the sinus venosus, the modelling of blood vessels, and the formation of forelimb buds, lung buds, dorsal pancreatic bud, lens, and otocyst. They also reveal that E9.5 to E10.5 spans a critical developmental period during which the RARs are required for trachea formation, lung branching morphogenesis, patterning of great arteries derived from aortic arches, closure of the optic fissure, and growth of inner ear structures and of facial processes. Comparing the phenotypes of mutants lacking the 3 RARs with that of mutants deprived of all-trans retinoic acid (ATRA) synthesising enzymes establishes that cardiac looping is the earliest known morphogenetic event requiring a functional ATRA-activated RAR signalling pathway. Full article
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Review

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16 pages, 2367 KiB  
Review
Quantitative Image Processing for Three-Dimensional Episcopic Images of Biological Structures: Current State and Future Directions
by Natalie Aroha Holroyd, Claire Walsh, Lucie Gourmet and Simon Walker-Samuel
Biomedicines 2023, 11(3), 909; https://doi.org/10.3390/biomedicines11030909 - 15 Mar 2023
Cited by 1 | Viewed by 1964
Abstract
Episcopic imaging using techniques such as High Resolution Episcopic Microscopy (HREM) and its variants, allows biological samples to be visualized in three dimensions over a large field of view. Quantitative analysis of episcopic image data is undertaken using a range of methods. In [...] Read more.
Episcopic imaging using techniques such as High Resolution Episcopic Microscopy (HREM) and its variants, allows biological samples to be visualized in three dimensions over a large field of view. Quantitative analysis of episcopic image data is undertaken using a range of methods. In this systematic review, we look at trends in quantitative analysis of episcopic images and discuss avenues for further research. Papers published between 2011 and 2022 were analyzed for details about quantitative analysis approaches, methods of image annotation and choice of image processing software. It is shown that quantitative processing is becoming more common in episcopic microscopy and that manual annotation is the predominant method of image analysis. Our meta-analysis highlights where tools and methods require further development in this field, and we discuss what this means for the future of quantitative episcopic imaging, as well as how annotation and quantification may be automated and standardized across the field. Full article
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