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Branciforti F, Salvi M, D’Agostino F, Marzola F, Cornacchia S, De Titta MO, Mastronuzzi G, Meloni I, Moschetta M, Porciani N, Sciscenti F, Spertini A, Spilla A, Zagaria I, Deloria AJ, Deng S, Haindl R, Szakacs G, Csiszar A, Liu M, Drexler W, Molinari F, Meiburger KM. Segmentation and Multi-Timepoint Tracking of 3D Cancer Organoids from Optical Coherence Tomography Images Using Deep Neural Networks. Diagnostics (Basel) 2024; 14:1217. [PMID: 38928633 PMCID: PMC11203156 DOI: 10.3390/diagnostics14121217] [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: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Recent years have ushered in a transformative era in in vitro modeling with the advent of organoids, three-dimensional structures derived from stem cells or patient tumor cells. Still, fully harnessing the potential of organoids requires advanced imaging technologies and analytical tools to quantitatively monitor organoid growth. Optical coherence tomography (OCT) is a promising imaging modality for organoid analysis due to its high-resolution, label-free, non-destructive, and real-time 3D imaging capabilities, but accurately identifying and quantifying organoids in OCT images remain challenging due to various factors. Here, we propose an automatic deep learning-based pipeline with convolutional neural networks that synergistically includes optimized preprocessing steps, the implementation of a state-of-the-art deep learning model, and ad-hoc postprocessing methods, showcasing good generalizability and tracking capabilities over an extended period of 13 days. The proposed tracking algorithm thoroughly documents organoid evolution, utilizing reference volumes, a dual branch analysis, key attribute evaluation, and probability scoring for match identification. The proposed comprehensive approach enables the accurate tracking of organoid growth and morphological changes over time, advancing organoid analysis and serving as a solid foundation for future studies for drug screening and tumor drug sensitivity detection based on organoids.
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Affiliation(s)
- Francesco Branciforti
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Massimo Salvi
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Filippo D’Agostino
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Francesco Marzola
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Sara Cornacchia
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Maria Olimpia De Titta
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Girolamo Mastronuzzi
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Isotta Meloni
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Miriam Moschetta
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Niccolò Porciani
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Fabrizio Sciscenti
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Alessandro Spertini
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Andrea Spilla
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Ilenia Zagaria
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Abigail J. Deloria
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Shiyu Deng
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Richard Haindl
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Gergely Szakacs
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (G.S.); (A.C.)
| | - Agnes Csiszar
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (G.S.); (A.C.)
| | - Mengyang Liu
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Filippo Molinari
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Kristen M. Meiburger
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
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Leitgeb R, Placzek F, Rank E, Krainz L, Haindl R, Li Q, Liu M, Andreana M, Unterhuber A, Schmoll T, Drexler W. Enhanced medical diagnosis for dOCTors: a perspective of optical coherence tomography. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210150-PER. [PMID: 34672145 PMCID: PMC8528212 DOI: 10.1117/1.jbo.26.10.100601] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/23/2021] [Indexed: 05/17/2023]
Abstract
SIGNIFICANCE After three decades, more than 75,000 publications, tens of companies being involved in its commercialization, and a global market perspective of about USD 1.5 billion in 2023, optical coherence tomography (OCT) has become one of the fastest successfully translated imaging techniques with substantial clinical and economic impacts and acceptance. AIM Our perspective focuses on disruptive forward-looking innovations and key technologies to further boost OCT performance and therefore enable significantly enhanced medical diagnosis. APPROACH A comprehensive review of state-of-the-art accomplishments in OCT has been performed. RESULTS The most disruptive future OCT innovations include imaging resolution and speed (single-beam raster scanning versus parallelization) improvement, new implementations for dual modality or even multimodality systems, and using endogenous or exogenous contrast in these hybrid OCT systems targeting molecular and metabolic imaging. Aside from OCT angiography, no other functional or contrast enhancing OCT extension has accomplished comparable clinical and commercial impacts. Some more recently developed extensions, e.g., optical coherence elastography, dynamic contrast OCT, optoretinography, and artificial intelligence enhanced OCT are also considered with high potential for the future. In addition, OCT miniaturization for portable, compact, handheld, and/or cost-effective capsule-based OCT applications, home-OCT, and self-OCT systems based on micro-optic assemblies or photonic integrated circuits will revolutionize new applications and availability in the near future. Finally, clinical translation of OCT including medical device regulatory challenges will continue to be absolutely essential. CONCLUSIONS With its exquisite non-invasive, micrometer resolution depth sectioning capability, OCT has especially revolutionized ophthalmic diagnosis and hence is the fastest adopted imaging technology in the history of ophthalmology. Nonetheless, OCT has not been completely exploited and has substantial growth potential-in academics as well as in industry. This applies not only to the ophthalmic application field, but also especially to the original motivation of OCT to enable optical biopsy, i.e., the in situ imaging of tissue microstructure with a resolution approaching that of histology but without the need for tissue excision.
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Affiliation(s)
- Rainer Leitgeb
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Medical University of Vienna, Christian Doppler Laboratory OPTRAMED, Vienna, Austria
| | - Fabian Placzek
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Elisabet Rank
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Lisa Krainz
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Richard Haindl
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Qian Li
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Mengyang Liu
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Marco Andreana
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Angelika Unterhuber
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Tilman Schmoll
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Carl Zeiss Meditec, Inc., Dublin, California, United States
| | - Wolfgang Drexler
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Address all correspondence to Wolfgang Drexler,
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