1
|
Kvåle Løvmo M, Deng S, Moser S, Leitgeb R, Drexler W, Ritsch-Marte M. Ultrasound-induced reorientation for multi-angle optical coherence tomography. Nat Commun 2024; 15:2391. [PMID: 38493195 PMCID: PMC10944478 DOI: 10.1038/s41467-024-46506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Organoid and spheroid technology provide valuable insights into developmental biology and oncology. Optical coherence tomography (OCT) is a label-free technique that has emerged as an excellent tool for monitoring the structure and function of these samples. However, mature organoids are often too opaque for OCT. Access to multi-angle views is highly desirable to overcome this limitation, preferably with non-contact sample handling. To fulfil these requirements, we present an ultrasound-induced reorientation method for multi-angle-OCT, which employs a 3D-printed acoustic trap inserted into an OCT imaging system, to levitate and reorient zebrafish larvae and tumor spheroids in a controlled and reproducible manner. A model-based algorithm was developed for the physically consistent fusion of multi-angle data from a priori unknown angles. We demonstrate enhanced penetration depth in the joint 3D-recovery of reflectivity, attenuation, refractive index, and position registration for zebrafish larvae, creating an enabling tool for future applications in volumetric imaging.
Collapse
Affiliation(s)
- Mia Kvåle Løvmo
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Shiyu Deng
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Simon Moser
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rainer Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Monika Ritsch-Marte
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
2
|
Zhou KC, Harfouche M, Cooke CL, Park J, Konda PC, Kreiss L, Kim K, Jönsson J, Doman T, Reamey P, Saliu V, Cook CB, Zheng M, Bechtel JP, Bègue A, McCarroll M, Bagwell J, Horstmeyer G, Bagnat M, Horstmeyer R. Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second. NATURE PHOTONICS 2023; 17:442-450. [PMID: 37808252 PMCID: PMC10552607 DOI: 10.1038/s41566-023-01171-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/03/2023] [Indexed: 10/10/2023]
Abstract
Wide field of view microscopy that can resolve 3D information at high speed and spatial resolution is highly desirable for studying the behaviour of freely moving model organisms. However, it is challenging to design an optical instrument that optimises all these properties simultaneously. Existing techniques typically require the acquisition of sequential image snapshots to observe large areas or measure 3D information, thus compromising on speed and throughput. Here, we present 3D-RAPID, a computational microscope based on a synchronized array of 54 cameras that can capture high-speed 3D topographic videos over an area of 135 cm2, achieving up to 230 frames per second at spatiotemporal throughputs exceeding 5 gigapixels per second. 3D-RAPID employs a 3D reconstruction algorithm that, for each synchronized snapshot, fuses all 54 images into a composite that includes a co-registered 3D height map. The self-supervised 3D reconstruction algorithm trains a neural network to map raw photometric images to 3D topography using stereo overlap redundancy and ray-propagation physics as the only supervision mechanism. The resulting reconstruction process is thus robust to generalization errors and scales to arbitrarily long videos from arbitrarily sized camera arrays. We demonstrate the broad applicability of 3D-RAPID with collections of several freely behaving organisms, including ants, fruit flies, and zebrafish larvae.
Collapse
Affiliation(s)
- Kevin C. Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
- Current affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Mark Harfouche
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Colin L. Cooke
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Jaehee Park
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Pavan C. Konda
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lucas Kreiss
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Kanghyun Kim
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Joakim Jönsson
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas Doman
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Paul Reamey
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Veton Saliu
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Clare B. Cook
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Maxwell Zheng
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | | | - Aurélien Bègue
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
| | - Matthew McCarroll
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Jennifer Bagwell
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | | | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Roarke Horstmeyer
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Ramona Optics Inc., 1000 W Main St., Durham, NC 27701, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| |
Collapse
|
3
|
Yasuhiko O, Takeuchi K. In-silico clearing approach for deep refractive index tomography by partial reconstruction and wave-backpropagation. LIGHT, SCIENCE & APPLICATIONS 2023; 12:101. [PMID: 37105955 PMCID: PMC10140380 DOI: 10.1038/s41377-023-01144-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/08/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Refractive index (RI) is considered to be a fundamental physical and biophysical parameter in biological imaging, as it governs light-matter interactions and light propagation while reflecting cellular properties. RI tomography enables volumetric visualization of RI distribution, allowing biologically relevant analysis of a sample. However, multiple scattering (MS) and sample-induced aberration (SIA) caused by the inhomogeneity in RI distribution of a thick sample make its visualization challenging. This paper proposes a deep RI tomographic approach to overcome MS and SIA and allow the enhanced reconstruction of thick samples compared to that enabled by conventional linear-model-based RI tomography. The proposed approach consists of partial RI reconstruction using multiple holograms acquired with angular diversity and their backpropagation using the reconstructed partial RI map, which unambiguously reconstructs the next partial volume. Repeating this operation efficiently reconstructs the entire RI tomogram while suppressing MS and SIA. We visualized a multicellular spheroid of diameter 140 µm within minutes of reconstruction, thereby demonstrating the enhanced deep visualization capability and computational efficiency of the proposed method compared to those of conventional RI tomography. Furthermore, we quantified the high-RI structures and morphological changes inside multicellular spheroids, indicating that the proposed method can retrieve biologically relevant information from the RI distribution. Benefitting from the excellent biological interpretability of RI distributions, the label-free deep visualization capability of the proposed method facilitates a noninvasive understanding of the architecture and time-course morphological changes of thick multicellular specimens.
Collapse
Affiliation(s)
- Osamu Yasuhiko
- Central Research Laboratory, Hamamatsu Photonics K.K, 5000 Hirakuchi, Hamakita-ku, Hamamatsu, 434-8601, Shizuoka, Japan.
| | - Kozo Takeuchi
- Central Research Laboratory, Hamamatsu Photonics K.K, 5000 Hirakuchi, Hamakita-ku, Hamamatsu, 434-8601, Shizuoka, Japan.
| |
Collapse
|
4
|
Lichtenegger A, Baumann B, Yasuno Y. Optical Coherence Tomography Is a Promising Tool for Zebrafish-Based Research-A Review. Bioengineering (Basel) 2022; 10:5. [PMID: 36671577 PMCID: PMC9854701 DOI: 10.3390/bioengineering10010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The zebrafish is an established vertebrae model in the field of biomedical research. With its small size, rapid maturation time and semi-transparency at early development stages, it has proven to be an important animal model, especially for high-throughput studies. Three-dimensional, high-resolution, non-destructive and label-free imaging techniques are perfectly suited to investigate these animals over various development stages. Optical coherence tomography (OCT) is an interferometric-based optical imaging technique that has revolutionized the diagnostic possibilities in the field of ophthalmology and has proven to be a powerful tool for many microscopic applications. Recently, OCT found its way into state-of-the-art zebrafish-based research. This review article gives an overview and a discussion of the relevant literature and an outlook for this emerging field.
Collapse
Affiliation(s)
- Antonia Lichtenegger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria
- Computational Optics Group, University of Tsukuba, Tsukuba 305-8573, Japan
| | - Bernhard Baumann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba 305-8573, Japan
| |
Collapse
|