1
|
Holroyd NA, Walsh C, Gourmet L, Walker-Samuel S. Quantitative Image Processing for Three-Dimensional Episcopic Images of Biological Structures: Current State and Future Directions. Biomedicines 2023; 11:909. [PMID: 36979887 PMCID: PMC10045950 DOI: 10.3390/biomedicines11030909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
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.
Collapse
Affiliation(s)
| | - Claire Walsh
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK
| | - Lucie Gourmet
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
| | - Simon Walker-Samuel
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
| |
Collapse
|
2
|
High-Resolution Episcopic Microscopy (HREM): Looking Back on 13 Years of Successful Generation of Digital Volume Data of Organic Material for 3D Visualisation and 3D Display. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9183826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
High-resolution episcopic microscopy (HREM) is an imaging technique that permits the simple and rapid generation of three-dimensional (3D) digital volume data of histologically embedded and physically sectioned specimens. The data can be immediately used for high-detail 3D analysis of a broad variety of organic materials with all modern methods of 3D visualisation and display. Since its first description in 2006, HREM has been adopted as a method for exploring organic specimens in many fields of science, and it has recruited a slowly but steadily growing user community. This review aims to briefly introduce the basic principles of HREM data generation and to provide an overview of scientific publications that have been published in the last 13 years involving HREM imaging. The studies to which we refer describe technical details and specimen-specific protocols, and provide examples of the successful use of HREM in biological, biomedical and medical research. Finally, the limitations, potentials and anticipated further improvements are briefly outlined.
Collapse
|
3
|
Visualising the Cardiovascular System of Embryos of Biomedical Model Organisms with High Resolution Episcopic Microscopy (HREM). J Cardiovasc Dev Dis 2018; 5:jcdd5040058. [PMID: 30558275 PMCID: PMC6306920 DOI: 10.3390/jcdd5040058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
The article will briefly introduce the high-resolution episcopic microscopy (HREM) technique and will focus on its potential for researching cardiovascular development and remodelling in embryos of biomedical model organisms. It will demonstrate the capacity of HREM for analysing the cardiovascular system of normally developed and genetically or experimentally malformed zebrafish, frog, chick and mouse embryos in the context of the whole specimen and will exemplarily show the possibilities HREM offers for comprehensive visualisation of the vasculature of adult human skin. Finally, it will provide examples of the successful application of HREM for identifying cardiovascular malformations in genetically altered mouse embryos produced in the deciphering the mechanisms of developmental disorders (DMDD) program.
Collapse
|
4
|
Geyer SH, Reissig LF, Hüsemann M, Höfle C, Wilson R, Prin F, Szumska D, Galli A, Adams DJ, White J, Mohun TJ, Weninger WJ. Morphology, topology and dimensions of the heart and arteries of genetically normal and mutant mouse embryos at stages S21-S23. J Anat 2017; 231:600-614. [PMID: 28776665 PMCID: PMC5603791 DOI: 10.1111/joa.12663] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2017] [Indexed: 12/23/2022] Open
Abstract
Accurate identification of abnormalities in the mouse embryo depends not only on comparisons with appropriate, developmental stage‐matched controls, but also on an appreciation of the range of anatomical variation that can be expected during normal development. Here we present a morphological, topological and metric analysis of the heart and arteries of mouse embryos harvested on embryonic day (E)14.5, based on digital volume data of whole embryos analysed by high‐resolution episcopic microscopy (HREM). By comparing data from 206 genetically normal embryos, we have analysed the range and frequency of normal anatomical variations in the heart and major arteries across Theiler stages S21–S23. Using this, we have identified abnormalities in these structures among 298 embryos from mutant mouse lines carrying embryonic lethal gene mutations produced for the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme. We present examples of both commonly occurring abnormal phenotypes and novel pathologies that most likely alter haemodynamics in these genetically altered mouse embryos. Our findings offer a reference baseline for identifying accurately abnormalities of the heart and arteries in embryos that have largely completed organogenesis.
Collapse
Affiliation(s)
- Stefan H Geyer
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Lukas F Reissig
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Markus Hüsemann
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Cordula Höfle
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Geyer SH, Maurer-Gesek B, Reissig LF, Weninger WJ. High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials. J Vis Exp 2017. [PMID: 28715372 PMCID: PMC5609318 DOI: 10.3791/56071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm3. Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material.
Collapse
Affiliation(s)
- Stefan H Geyer
- Division of Anatomy, Center for Anatomy and Cell Biology & MIC, Medical University of Vienna
| | - Barbara Maurer-Gesek
- Division of Anatomy, Center for Anatomy and Cell Biology & MIC, Medical University of Vienna
| | - Lukas F Reissig
- Division of Anatomy, Center for Anatomy and Cell Biology & MIC, Medical University of Vienna
| | - Wolfgang J Weninger
- Division of Anatomy, Center for Anatomy and Cell Biology & MIC, Medical University of Vienna;
| |
Collapse
|
6
|
Weninger WJ, Geyer SH, Martineau A, Galli A, Adams DJ, Wilson R, Mohun TJ. Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy. Dis Model Mech 2015; 7:1143-52. [PMID: 25256713 PMCID: PMC4174525 DOI: 10.1242/dmm.016337] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The arrival of simple and reliable methods for 3D imaging of mouse embryos has opened the possibility of analysing normal and abnormal development in a far more systematic and comprehensive manner than has hitherto been possible. This will not only help to extend our understanding of normal tissue and organ development but, by applying the same approach to embryos from genetically modified mouse lines, such imaging studies could also transform our knowledge of gene function in embryogenesis and the aetiology of developmental disorders. The International Mouse Phenotyping Consortium is coordinating efforts to phenotype single gene knockouts covering the entire mouse genome, including characterising developmental defects for those knockout lines that prove to be embryonic lethal. Here, we present a pilot study of 34 such lines, utilising high-resolution episcopic microscopy (HREM) for comprehensive 2D and 3D imaging of homozygous null embryos and their wild-type littermates. We present a simple phenotyping protocol that has been developed to take advantage of the high-resolution images obtained by HREM and that can be used to score tissue and organ abnormalities in a reliable manner. Using this approach with embryos at embryonic day 14.5, we show the wide range of structural abnormalities that are likely to be detected in such studies and the variability in phenotypes between sibling homozygous null embryos.
Collapse
Affiliation(s)
- Wolfgang J Weninger
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, 1090 Wien, Austria.
| | - Stefan H Geyer
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, 1090 Wien, Austria
| | | | | | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Robert Wilson
- MRC National Institute for Medical Research, London NW7 1AA, UK
| | - Timothy J Mohun
- MRC National Institute for Medical Research, London NW7 1AA, UK
| |
Collapse
|
7
|
Wiedner M, Tinhofer IE, Kamolz LP, Seyedian Moghaddam A, Justich I, Liegl-Atzwanger B, Bubalo V, Weninger WJ, Lumenta DB. Simultaneous dermal matrix and autologous split-thickness skin graft transplantation in a porcine wound model: a three-dimensional histological analysis of revascularization. Wound Repair Regen 2015; 22:749-54. [PMID: 25358670 DOI: 10.1111/wrr.12233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 09/04/2014] [Indexed: 01/01/2023]
Abstract
Despite the popularity of a simultaneous application of dermal matrices and split-thickness skin grafts, scarce evidence exists about the process of revascularization involved. In this study, we aimed at analyzing the progression of revascularization by high-resolution episcopic microscopy (HREM) in a porcine excisional wound model. Following the surgical procedure creating 5 × 5 cm(2) full-thickness defects on the back, one area was covered with an autologous split-thickness skin graft alone (control group), the other with a collagen-elastin dermal matrix plus split-thickness skin graft (dermal matrix group). Two skin biopsies per each group and location were performed on day 5, 10, 15, and 28 postoperatively and separately processed for H&E as well as HREM. The dermal layer was thicker in the dermal matrix group vs. control on day 5 and 28. No differences were found for revascularization by conventional histology. In HREM, the dermal matrix did not appear to decelerate the revascularization process. The presence of the dermal matrix could be distinguished until day 15. By day 28, the structure of the dermal matrix could no longer be delineated and was replaced by autologous tissue. As assessed by conventional histology and confirmed by HREM, the revascularization process was comparable in both groups, notably with regard to the vertical ingrowth of sprouting vessels. The presented technique of HREM is a valuable addition for analyzing small vessel sprouting in dermal matrices in the future.
Collapse
Affiliation(s)
- Maria Wiedner
- Research Unit for Tissue Regeneration, Repair, and Reconstruction, Division of Plastic, Aesthetic, and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
High-resolution episcopic microscopy (HREM): A useful technique for research in wound care. Ann Anat 2015; 197:3-10. [DOI: 10.1016/j.aanat.2014.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/24/2014] [Accepted: 10/13/2014] [Indexed: 12/15/2022]
|
9
|
Geyer SH, Nöhammer MM, Mathä M, Reissig L, Tinhofer IE, Weninger WJ. High-resolution episcopic microscopy (HREM): a tool for visualizing skin biopsies. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:1356-64. [PMID: 25198556 DOI: 10.1017/s1431927614013063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We evaluate the usefulness of digital volume data produced with the high-resolution episcopic microscopy (HREM) method for visualizing the three-dimensional (3D) arrangement of components of human skin, and present protocols designed for processing skin biopsies for HREM data generation. A total of 328 biopsies collected from normally appearing skin and from a melanocytic nevus were processed. Cuboidal data volumes with side lengths of ~2×3×6 mm3 and voxel sizes of 1.07×1.07×1.5 µm3 were produced. HREM data fit ideally for visualizing the epidermis at large, and for producing highly detailed volume and surface-rendered 3D representations of the dermal and hypodermal components at a structural level. The architecture of the collagen fiber bundles and the spatial distribution of nevus cells can be easily visualized with volume-rendering algorithms. We conclude that HREM has great potential to serve as a routine tool for researching and diagnosing skin pathologies.
Collapse
Affiliation(s)
- Stefan H Geyer
- 1MRC National Institute for Medical Research,London,NW7 1AA,UK
| | - Maria M Nöhammer
- 2Centre for Anatomy and Cell Biology,Medical University of Vienna,Waehringer Street 13,A-1090 Vienna,Austria
| | - Markus Mathä
- 2Centre for Anatomy and Cell Biology,Medical University of Vienna,Waehringer Street 13,A-1090 Vienna,Austria
| | - Lukas Reissig
- 2Centre for Anatomy and Cell Biology,Medical University of Vienna,Waehringer Street 13,A-1090 Vienna,Austria
| | - Ines E Tinhofer
- 2Centre for Anatomy and Cell Biology,Medical University of Vienna,Waehringer Street 13,A-1090 Vienna,Austria
| | - Wolfgang J Weninger
- 2Centre for Anatomy and Cell Biology,Medical University of Vienna,Waehringer Street 13,A-1090 Vienna,Austria
| |
Collapse
|