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, 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
|
5
|
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]
|
6
|
Liu M, Maurer B, Hermann B, Zabihian B, Sandrian MG, Unterhuber A, Baumann B, Zhang EZ, Beard PC, Weninger WJ, Drexler W. Dual modality optical coherence and whole-body photoacoustic tomography imaging of chick embryos in multiple development stages. BIOMEDICAL OPTICS EXPRESS 2014; 5:3150-9. [PMID: 25401028 PMCID: PMC4230868 DOI: 10.1364/boe.5.003150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 05/19/2023]
Abstract
Chick embryos are an important animal model for biomedical studies. The visualization of chick embryos, however, is limited mostly to postmortem sectional imaging methods. In this work, we present a dual modality optical imaging system that combines swept-source optical coherence tomography and whole-body photoacoustic tomography, and apply it to image chick embryos at three different development stages. The explanted chick embryos were imaged in toto with complementary contrast from both optical scattering and optical absorption. The results serve as a prelude to the use of the dual modality system in longitudinal whole-body monitoring of chick embryos in ovo.
Collapse
Affiliation(s)
- Mengyang Liu
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Barbara Maurer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Währinger Straße 13, Vienna 1090, Austria
| | - Boris Hermann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Behrooz Zabihian
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Michelle G. Sandrian
- Department of Ophthalmology, University of Pittsburgh, Eye & Ear Institute, 203 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Angelika Unterhuber
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Bernhard Baumann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Edward Z. Zhang
- Department of Medical Physics and Bioengineering, University College London, Shropshire House, 11-20 Capper Street, London WC1E 6JA, UK
| | - Paul C. Beard
- Department of Medical Physics and Bioengineering, University College London, Shropshire House, 11-20 Capper Street, London WC1E 6JA, UK
| | - Wolfgang J. Weninger
- Center for Anatomy and Cell Biology, Medical University of Vienna, Währinger Straße 13, Vienna 1090, Austria
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, AKH 4L, Währinger Gürtel 18-20, Vienna 1090, Austria
| |
Collapse
|