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Geyer SH, Ceci Ginistrelli L, Ilmer T, Schwendt KM, Mendjan S, Weninger WJ. Three-dimensional structural and metric characterisation of cardioids. Front Cell Dev Biol 2024; 12:1426043. [PMID: 39119041 PMCID: PMC11306051 DOI: 10.3389/fcell.2024.1426043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Exact three-dimensional (3D) structural information of developing organoids is key for optimising organoid generation and for studying experimental outcomes in organoid models. We set up a 3D imaging technique and studied complexly arranged native and experimentally challenged cardioids of two stages of remodelling. The imaging technique we employed is S-HREM (Scanning High Resolution Episcopic Microscopy), a variant of HREM, which captures multiple images of subsequently exposed surfaces of resin blocks and automatically combines them to large sized digital volume data of voxels sizes below 1 μm3. We provide precise volumetric information of the examined specimens and their single components and comparisons between stages in terms of volume and micro- and macroanatomic structure. We describe the 3D arrangement and lining of different types of cavities and their changes between day 10 and day 14 and map the various cell types to their precise spatial and structural environment. Exemplarily, we conducted semiautomatic counts of nuclei. In cryo-injured cardioids, we examined the extension and composition of the injured areas. Our results demonstrate the high quality and the great potential of digital volume data produced with S-HREM. It also provides sound metric and structural information, which assists production of native and experimentally challenged left ventricle cardioids and interpretation of their structural remodelling.
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Affiliation(s)
- Stefan H. Geyer
- Division of Anatomy, Center for Anatomy and Cell Biology, MIC, Medical University of Vienna, Vienna, Austria
| | - Lavinia Ceci Ginistrelli
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Tobias Ilmer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Karoline M. Schwendt
- Division of Anatomy, Center for Anatomy and Cell Biology, MIC, Medical University of Vienna, Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang J. Weninger
- Division of Anatomy, Center for Anatomy and Cell Biology, MIC, Medical University of Vienna, Vienna, Austria
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Mitchell B, Mu E, Currey L, Whitehead D, Walters S, Thor S, Kasherman M, Piper M. A protocol for high-resolution episcopic microscopy and 3D volumetric analyses of the adult mouse brain. Neurosci Lett 2024; 824:137675. [PMID: 38355003 DOI: 10.1016/j.neulet.2024.137675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
The rapid evolution of different imaging modalities in the last two decades has enabled the investigation of the role of different genes in development and disease to be studied in a range of model organisms. However, selection of the appropriate imaging technique depends on a number of constraints, including cost, time, image resolution, size of the sample, computational complexity and processing power. Here, we use the adult mouse central nervous system to investigate whether High-Resolution Episcopic Microscopy (HREM) can provide an effective means to study the volume of individual subregions within the brain. We find that HREM can provide precise volume quantification of different structures within the mouse brain, albeit with limitations regarding the time involved for analysis and the necessity of some estimations.
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Affiliation(s)
- Benjamin Mitchell
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Mu
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Laura Currey
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darryl Whitehead
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shaun Walters
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefan Thor
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Katharina Gaus Light Microscopy Facility, Division of Research, Lowy Cancer Research Center C25, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia.
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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.
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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
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Reissig LF, Geyer SH, Winkler V, Preineder E, Prin F, Wilson R, Galli A, Tudor C, White JK, Mohun TJ, Weninger WJ. Detailed characterizations of cranial nerve anatomy in E14.5 mouse embryos/fetuses and their use as reference for diagnosing subtle, but potentially lethal malformations in mutants. Front Cell Dev Biol 2022; 10:1006620. [PMID: 36438572 PMCID: PMC9682249 DOI: 10.3389/fcell.2022.1006620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/28/2022] [Indexed: 01/03/2024] Open
Abstract
Careful phenotype analysis of genetically altered mouse embryos/fetuses is vital for deciphering the function of pre- and perinatally lethal genes. Usually this involves comparing the anatomy of mutants with that of wild types of identical developmental stages. Detailed three dimensional information on regular cranial nerve (CN) anatomy of prenatal mice is very scarce. We therefore set out to provide such information to be used as reference data and selected mutants to demonstrate its potential for diagnosing CN abnormalities. Digital volume data of 152 wild type mice, harvested on embryonic day (E)14.5 and of 18 mutants of the Col4a2, Arid1b, Rpgrip1l and Cc2d2a null lines were examined. The volume data had been created with High Resolution Episcopic Microscopy (HREM) as part of the deciphering the mechanisms of developmental disorders (DMDD) program. Employing volume and surface models, oblique slicing and digital measuring tools, we provide highly detailed anatomic descriptions of the CNs and measurements of the diameter of selected segments. Specifics of the developmental stages of E14.5 mice and anatomic norm variations were acknowledged. Using the provided data as reference enabled us to objectively diagnose CN abnormalities, such as abnormal formation of CN3 (Col4a2), neuroma of the motor portion of CN5 (Arid1b), thinning of CN7 (Rpgrip1l) and abnormal topology of CN12 (Cc2d2a). Although, in a first glimpse perceived as unspectacular, defects of the motor CN5 or CN7, like enlargement or thinning can cause death of newborns, by hindering feeding. Furthermore, abnormal topology of CN12 was recently identified as a highly reliable marker for low penetrating, but potentially lethal defects of the central nervous system.
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Affiliation(s)
- Lukas F. Reissig
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Stefan H. Geyer
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Viola Winkler
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Ester Preineder
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Fabrice Prin
- The Francis Crick Institute, London, United Kingdom
| | | | | | | | | | | | - Wolfgang J. Weninger
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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Handschuh S, Glösmann M. Mouse embryo phenotyping using X-ray microCT. Front Cell Dev Biol 2022; 10:949184. [PMID: 36187491 PMCID: PMC9523164 DOI: 10.3389/fcell.2022.949184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.
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Visualizing 3D Embryo and Tissue Morphology—A Decade of Using High-Resolution Episcopic Microscopy (HREM) in Biomedical Imaging. Biomedicines 2022; 10:biomedicines10051123. [PMID: 35625860 PMCID: PMC9139051 DOI: 10.3390/biomedicines10051123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
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