1
|
Chen W, Wang H. OCTSharp: an open-source and real-time OCT imaging software based on C. BIOMEDICAL OPTICS EXPRESS 2023; 14:6060-6071. [PMID: 38021120 PMCID: PMC10659780 DOI: 10.1364/boe.505308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Optical coherence tomography (OCT) demands massive data processing and real-time displaying during high-speed imaging. Current OCT imaging software is predominantly based on C++, aiming to maximize performance through low-level hardware management. However, the steep learning curve of C++ hinders agile prototyping, particularly for research purposes. Moreover, manual memory management poses challenges for novice developers and may lead to potential security issues. To address these limitations, OCTSharp is developed as an open-source OCT software based on the memory-safe language C#. Within the managed C# environment, OCTSharp offers synchronized hardware control, minimal memory management, and GPU-based parallel processing. The software has been thoroughly tested and proven capable of supporting real-time image acquisition, processing, and visualization with spectral-domain OCT systems equipped with the latest advanced hardware. With these enhancements, OCTSharp is positioned to serve as an open-source platform tailored for various applications.
Collapse
Affiliation(s)
- Weihao Chen
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
- Department of Biology, Miami University, Oxford, OH, USA
| | - Hui Wang
- Department of Biology, Miami University, Oxford, OH, USA
- Department of Electrical and Computer Engineering Miami University, Oxford, OH, USA
| |
Collapse
|
2
|
Brunet J, Cook AC, Walsh CL, Cranley J, Tafforeau P, Engel K, Berruyer C, O’Leary EB, Bellier A, Torii R, Werlein C, Jonigk DD, Ackermann M, Dollman K, Lee PD. Multidimensional Analysis of the Adult Human Heart in Health and Disease using Hierarchical Phase-Contrast Tomography (HiP-CT). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561474. [PMID: 37873359 PMCID: PMC10592740 DOI: 10.1101/2023.10.09.561474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP-CT), using new (4th) generation synchrotron sources, potentially overcomes this limitation, allowing micron resolution imaging of intact adult organs with unprecedented detail. In this proof of principle study (n=2), we show the utility of HiP-CT to image whole adult human hearts ex-vivo: one 'control' without known cardiac disease and one with multiple known cardiopulmonary pathologies. The resulting multiscale imaging was able to demonstrate exemplars of anatomy in each cardiac segment along with novel findings in the cardiac conduction system, from gross (20 um/voxel) to cellular scale (2.2 um/voxel), non-destructively, thereby bridging the gap between macroscopic and microscopic investigations. We propose that the technique represents a significant step in virtual autopsy methods for studying structural heart disease, facilitating research into abnormalities across scales and age-groups. It opens up possibilities for understanding and treating disease; and provides a cardiac 'blueprint' with potential for in-silico simulation, device design, virtual surgical training, and bioengineered heart in the future.
Collapse
Affiliation(s)
- J. Brunet
- Department of Mechanical Engineering, University College London, London, UK
- European Synchrotron Radiation Facility, Grenoble, France
| | - A. C. Cook
- UCL Institute of Cardiovascular Science, London, UK
| | - C. L. Walsh
- Department of Mechanical Engineering, University College London, London, UK
| | - J. Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - P. Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France
| | - K. Engel
- Siemens Healthineers, Erlangen, Germany
| | - C. Berruyer
- Department of Mechanical Engineering, University College London, London, UK
- European Synchrotron Radiation Facility, Grenoble, France
| | - E. Burke O’Leary
- Department of Mechanical Engineering, University College London, London, UK
| | - A. Bellier
- Laboratoire d’Anatomie des Alpes Françaises (LADAF), Université Grenoble Alpes, Grenoble, F
| | - R. Torii
- Department of Mechanical Engineering, University College London, London, UK
| | - C. Werlein
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), German Lung Research Centre (DZL), Hannover, Germany
| | - D. D. Jonigk
- Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), German Lung Research Centre (DZL), Hannover, Germany
- Institute of Pathology, Aachen Medical University, RWTH Aachen, Germany
| | - M. Ackermann
- Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - K. Dollman
- European Synchrotron Radiation Facility, Grenoble, France
| | - P. D. Lee
- Department of Mechanical Engineering, University College London, London, UK
- Research Complex at Harwell, Didcot, UK
| |
Collapse
|
3
|
Dey R, Alexandrov S, Owens P, Kelly J, Phelan S, Leahy M. Skin cancer margin detection using nanosensitive optical coherence tomography and a comparative study with confocal microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:5654-5666. [PMID: 36733740 PMCID: PMC9872867 DOI: 10.1364/boe.474334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 05/08/2023]
Abstract
Excision biopsy and histology represent the gold standard for morphological investigation of the skin, in particular for cancer diagnostics. Nevertheless, a biopsy may alter the original morphology, usually requires several weeks for results, is non-repeatable on the same site and always requires an iatrogenic trauma. Hence, diagnosis and clinical management of diseases may be substantially improved by new non-invasive imaging techniques. Optical Coherence Tomography (OCT) is a non-invasive depth-resolved optical imaging modality based on low coherence interferometry that enables high-resolution, cross-sectional imaging in biological tissues and it can be used to obtain both structural and functional information. Beyond the resolution limit, it is not possible to detect structural and functional information using conventional OCT. In this paper, we present a recently developed technique, nanosensitive OCT (nsOCT), improved using broadband supercontinuum laser, and demonstrate nanoscale sensitivity to structural changes within ex vivo human skin tissue. The extended spectral bandwidth permitted access to a wider distribution of spatial frequencies and improved the dynamic range of the nsOCT. Firstly, we demonstrate numerical and experimental detection of a few nanometers structural difference using the nsOCT method from single B-scan images of phantoms with sub-micron periodic structures, acting like Bragg gratings, along the depth. Secondly, our study shows that nsOCT can distinguish nanoscale structural changes at the skin cancer margin from the healthy region in en face images at clinically relevant depths. Finally, we compare the nsOCT en face image with a high-resolution confocal microscopy image to confirm the structural differences between the healthy and lesional/cancerous regions, allowing the detection of the skin cancer margin.
Collapse
Affiliation(s)
- Rajib Dey
- Tissue Optics and Microcirculation Imaging (TOMI) Facility, National Biophotonics and Imaging Platform School of Physics, National University of Ireland, Galway, Galway, Ireland
| | - Sergey Alexandrov
- Tissue Optics and Microcirculation Imaging (TOMI) Facility, National Biophotonics and Imaging Platform School of Physics, National University of Ireland, Galway, Galway, Ireland
| | - Peter Owens
- Center for Microscopy and Imaging, National University of Ireland, Galway, Galway, Ireland
| | - Jack Kelly
- Plastic and Reconstructive Surgery, Galway University Hospital, Galway, Ireland
| | - Sine Phelan
- Department of Anatomic Pathology, Galway University Hospital and Department of Pathology, National University of Ireland, Galway, Galway, Ireland
| | - Martin Leahy
- Tissue Optics and Microcirculation Imaging (TOMI) Facility, National Biophotonics and Imaging Platform School of Physics, National University of Ireland, Galway, Galway, Ireland
- Institute of Photonic Sciences (ICFO), Barcelona, Spain
| |
Collapse
|