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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| Format: | Article |
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MDPI AG
2021-11-01
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| Series: | Biomedicines |
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| Online Access: | https://www.mdpi.com/2227-9059/9/11/1711 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:41:38Z |
| format | Article |
| id | doaj.art-ca09480fece248ccbc47be14e028a050 |
| institution | Directory Open Access Journal |
| issn | 2227-9059 |
| language | English |
| last_indexed | 2024-03-10T05:41:38Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomedicines |
| spelling | doaj.art-ca09480fece248ccbc47be14e028a0502023-11-22T22:32:18ZengMDPI AGBiomedicines2227-90592021-11-01911171110.3390/biomedicines9111711Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)Lukas F. Reissig0Stefan H. Geyer1Julia Rose2Fabrice Prin3Robert Wilson4Dorota Szumska5Antonella Galli6Catherine Tudor7Jacqueline K. White8Tim J. Mohun9Wolfgang J. Weninger10Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, AustriaDivision of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, AustriaDivision of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, AustriaCrick Advanced Light Microscopy Facility, The Francis Crick Institute, London NW1 1AT, UKThe Francis Crick Institute Mill Hill Laboratory, London NW7 1AA, UKWellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UKWellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UKWellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UKWellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UKThe Francis Crick Institute Mill Hill Laboratory, London NW7 1AA, UKDivision of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, AustriaHigh 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.https://www.mdpi.com/2227-9059/9/11/1711HREMartefactsblock face imaginghistologyembryogenetically engineered |
| spellingShingle | 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) Biomedicines HREM artefacts block face imaging histology embryo genetically engineered |
| title | 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_short | Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM) |
| title_sort | artefacts in volume data generated with high resolution episcopic microscopy hrem |
| topic | HREM artefacts block face imaging histology embryo genetically engineered |
| url | https://www.mdpi.com/2227-9059/9/11/1711 |
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