Biomedicines

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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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

episcopic imaging
phenotyping
bioimaging
high-resolution episcopic microscopy

Published Papers (2 papers)

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Research

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24 pages, 5569 KiB

Open AccessArticle

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 3 | Viewed by 1770

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 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

(This article belongs to the Special Issue Visualizing 3D Embryo and Tissue Morphology—A Decade of Using High-Resolution Episcopic Microscopy (HREM) in Biomedical Imaging, Volume II)

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Review

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16 pages, 2367 KiB

Open AccessReview

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 1546

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 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

(This article belongs to the Special Issue Visualizing 3D Embryo and Tissue Morphology—A Decade of Using High-Resolution Episcopic Microscopy (HREM) in Biomedical Imaging, Volume II)

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