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Liu Y, Dong J, Schmidt C, Boquet-Pujadas A, Extermann J, Unser M. Artifacts in optical projection tomography due to refractive-index mismatch: model and correction. OPTICS LETTERS 2022; 47:2618-2621. [PMID: 35648888 DOI: 10.1364/ol.457144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Optical projection tomography (OPT) is a powerful tool for three-dimensional (3D) imaging of mesoscopic samples. While it is able to achieve resolution of a few tens of microns over a sample volume of several cubic centimeters, the reconstructed images often suffer from artifacts caused by inaccurate calibration. In this work, we focus on the refractive-index mismatch between the sample and the surrounding medium. We derive a 3D cone-beam forward model of OPT that approximates the effect of refractive-index mismatch. We then implement a fast and efficient reconstruction method to correct for the induced seagull-shaped artifacts on experimental images of fluorescent beads.
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Belay B, Koivisto JT, Parraga J, Koskela O, Montonen T, Kellomäki M, Figueiras E, Hyttinen J. Optical projection tomography as a quantitative tool for analysis of cell morphology and density in 3D hydrogels. Sci Rep 2021; 11:6538. [PMID: 33753803 PMCID: PMC7985381 DOI: 10.1038/s41598-021-85996-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/05/2021] [Indexed: 01/29/2023] Open
Abstract
Assessing cell morphology and function, as well as biomaterial performance in cell cultures, is one of the key challenges in cell biology and tissue engineering (TE) research. In TE, there is an urgent need for methods to image actual three-dimensional (3D) cell cultures and access the living cells. This is difficult using established optical microscopy techniques such as wide-field or confocal microscopy. To address the problem, we have developed a new protocol using Optical Projection Tomography (OPT) to extract quantitative and qualitative measurements from hydrogel cell cultures. Using our tools, we demonstrated the method by analyzing cell response in three different hydrogel formulations in 3D with 1.5 mm diameter samples of: gellan gum (GG), gelatin functionalized gellan gum (gelatin-GG), and Geltrex. We investigated cell morphology, density, distribution, and viability in 3D living cells. Our results showed the usability of the method to quantify the cellular responses to biomaterial environment. We observed that an elongated morphology of cells, thus good material response, in gelatin-GG and Geltrex hydrogels compared with basic GG. Our results show that OPT has a sensitivity to assess in real 3D cultures the differences of cellular responses to the properties of biomaterials supporting the cells.
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Affiliation(s)
- Birhanu Belay
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland.
| | - Janne T Koivisto
- Biomaterials and Tissue Engineering Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Heart Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Parraga
- Biomaterials and Tissue Engineering Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Koskela
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland.,HAMK Smart Research Unit, Häme University of Applied Sciences, Hämeenlinna, Finland
| | - Toni Montonen
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland
| | - Minna Kellomäki
- Biomaterials and Tissue Engineering Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Jari Hyttinen
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland
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Koskela O, Montonen T, Belay B, Figueiras E, Pursiainen S, Hyttinen J. Gaussian Light Model in Brightfield Optical Projection Tomography. Sci Rep 2019; 9:13934. [PMID: 31558755 PMCID: PMC6763473 DOI: 10.1038/s41598-019-50469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.
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Affiliation(s)
- Olli Koskela
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland.
- HAMK Smart Research Unit, Häme University of Applied Sciences, Hämeenlinna, 13100, Finland.
| | - Toni Montonen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Birhanu Belay
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Foundation, Lisbon, 1400-038, Portugal
| | - Sampsa Pursiainen
- Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, 33014, Finland
| | - Jari Hyttinen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
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