Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)

High resolution episcopic microscopy (HREM) produces digital volume data by physically sectioning histologically processed specimens, while capturing images of the subsequently exposed block faces. Our study aims to systematically define the spectrum of typical artefacts inherent to HREM data and to...

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Autores principales:	Lukas F. Reissig, Stefan H. Geyer, Julia Rose, Fabrice Prin, Robert Wilson, Dorota Szumska, Antonella Galli, Catherine Tudor, Jacqueline K. White, Tim J. Mohun, Wolfgang J. Weninger
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	HREM artefacts block face imaging histology embryo genetically engineered Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ca09480fece248ccbc47be14e028a050
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spelling	oai:doaj.org-article:ca09480fece248ccbc47be14e028a0502021-11-25T16:51:06ZArtefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)10.3390/biomedicines91117112227-9059https://doaj.org/article/ca09480fece248ccbc47be14e028a0502021-11-01T00:00:00Zhttps://www.mdpi.com/2227-9059/9/11/1711https://doaj.org/toc/2227-9059High resolution episcopic microscopy (HREM) produces digital volume data by physically sectioning histologically processed specimens, while capturing images of the subsequently exposed block faces. Our study aims to systematically define the spectrum of typical artefacts inherent to HREM data and to research their effect on the interpretation of the phenotype of wildtype and mutant mouse embryos. A total of 607 (198 wildtypes, 409 mutants) HREM data sets of mouse embryos harvested at embryonic day (E) 14.5 were systematically and comprehensively examined. The specimens had been processed according to essentially identical protocols. Each data set comprised 2000 to 4000 single digital images. Voxel dimensions were 3 × 3 × 3 µm<sup>3</sup>. Using 3D volume models and virtual resections, we identified a number of characteristic artefacts and grouped them according to their most likely causality. Furthermore, we highlight those that affect the interpretation of embryo data and provide examples for artefacts mimicking tissue defects and structural pathologies. Our results aid in optimizing specimen preparation and data generation, are vital for the correct interpretation of HREM data and allow distinguishing tissue defects and pathologies from harmless artificial alterations. In particular, they enable correct diagnosis of pathologies in mouse embryos serving as models for deciphering the mechanisms of developmental disorders.Lukas F. ReissigStefan H. GeyerJulia RoseFabrice PrinRobert WilsonDorota SzumskaAntonella GalliCatherine TudorJacqueline K. WhiteTim J. MohunWolfgang J. WeningerMDPI AGarticleHREMartefactsblock face imaginghistologyembryogenetically engineeredBiology (General)QH301-705.5ENBiomedicines, Vol 9, Iss 1711, p 1711 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	HREM artefacts block face imaging histology embryo genetically engineered Biology (General) QH301-705.5
spellingShingle	HREM artefacts block face imaging histology embryo genetically engineered Biology (General) QH301-705.5 Lukas F. Reissig Stefan H. Geyer Julia Rose Fabrice Prin Robert Wilson Dorota Szumska Antonella Galli Catherine Tudor Jacqueline K. White Tim J. Mohun Wolfgang J. Weninger Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
description	High resolution episcopic microscopy (HREM) produces digital volume data by physically sectioning histologically processed specimens, while capturing images of the subsequently exposed block faces. Our study aims to systematically define the spectrum of typical artefacts inherent to HREM data and to research their effect on the interpretation of the phenotype of wildtype and mutant mouse embryos. A total of 607 (198 wildtypes, 409 mutants) HREM data sets of mouse embryos harvested at embryonic day (E) 14.5 were systematically and comprehensively examined. The specimens had been processed according to essentially identical protocols. Each data set comprised 2000 to 4000 single digital images. Voxel dimensions were 3 × 3 × 3 µm<sup>3</sup>. Using 3D volume models and virtual resections, we identified a number of characteristic artefacts and grouped them according to their most likely causality. Furthermore, we highlight those that affect the interpretation of embryo data and provide examples for artefacts mimicking tissue defects and structural pathologies. Our results aid in optimizing specimen preparation and data generation, are vital for the correct interpretation of HREM data and allow distinguishing tissue defects and pathologies from harmless artificial alterations. In particular, they enable correct diagnosis of pathologies in mouse embryos serving as models for deciphering the mechanisms of developmental disorders.
format	article
author	Lukas F. Reissig Stefan H. Geyer Julia Rose Fabrice Prin Robert Wilson Dorota Szumska Antonella Galli Catherine Tudor Jacqueline K. White Tim J. Mohun Wolfgang J. Weninger
author_facet	Lukas F. Reissig Stefan H. Geyer Julia Rose Fabrice Prin Robert Wilson Dorota Szumska Antonella Galli Catherine Tudor Jacqueline K. White Tim J. Mohun Wolfgang J. Weninger
author_sort	Lukas F. Reissig
title	Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
title_short	Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
title_full	Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
title_fullStr	Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
title_full_unstemmed	Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)
title_sort	artefacts in volume data generated with high resolution episcopic microscopy (hrem)
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/ca09480fece248ccbc47be14e028a050
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Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)

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