The Dresden in vivo OCT dataset for automatic middle ear segmentation.

Humans Algorithms Ear, Middle / diagnostic imaging Neural Networks, Computer Tomography, Optical Coherence / methods

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
26 Feb 2024
Historique:
received: 21 09 2023
accepted: 25 01 2024
medline: 28 2 2024
pubmed: 27 2 2024
entrez: 26 2 2024
Statut: epublish

Résumé

Endoscopic optical coherence tomography (OCT) offers a non-invasive approach to perform the morphological and functional assessment of the middle ear in vivo. However, interpreting such OCT images is challenging and time-consuming due to the shadowing of preceding structures. Deep neural networks have emerged as a promising tool to enhance this process in multiple aspects, including segmentation, classification, and registration. Nevertheless, the scarcity of annotated datasets of OCT middle ear images poses a significant hurdle to the performance of neural networks. We introduce the Dresden in vivo OCT Dataset of the Middle Ear (DIOME) featuring 43 OCT volumes from both healthy and pathological middle ears of 29 subjects. DIOME provides semantic segmentations of five crucial anatomical structures (tympanic membrane, malleus, incus, stapes and promontory), and sparse landmarks delineating the salient features of the structures. The availability of these data facilitates the training and evaluation of algorithms regarding various analysis tasks with middle ear OCT images, e.g. diagnostics.

Identifiants

DOI: 10.1038/s41597-024-03000-0 PMID: 38409278
pubmed: 38409278
doi: 10.1038/s41597-024-03000-0
pii: 10.1038/s41597-024-03000-0
doi:

Types de publication

Dataset Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

242

Informations de copyright

© 2024. The Author(s).

Références

Zwislocki, J. Normal function of the middle ear and its measurement. Audiology 21, 4–14 (1982).
doi: 10.3109/00206098209072723 pubmed: 7055478
Kirsten, L. et al. Endoscopic optical coherence tomography with wide field-of-view for the morphological and functional assessment of the human tympanic membrane. Journal of Biomedical Optics 24, 031017 (2018).
doi: 10.1117/1.JBO.24.3.031017 pubmed: 30516037 pmcid: 6975278
Morgenstern, J. et al. Endoscopic optical coherence tomography for evaluation of success of tympanoplasty. Otology & Neurotology 41, e901–e905 (2020).
doi: 10.1097/MAO.0000000000002486
Steuer, S. et al. In vivo microstructural investigation of the human tympanic membrane by endoscopic polarization-sensitive optical coherence tomography. Journal of Biomedical Optics 28, 121203 (2023).
doi: 10.1117/1.JBO.28.12.121203 pubmed: 37007626 pmcid: 10050973
MacDougall, D., Farrell, J., Brown, J., Bance, M. & Adamson, R. Long-range, wide-field swept-source optical coherence tomography with GPU accelerated digital lock-in doppler vibrography for real-time, in vivo middle ear diagnostics. Biomedical Optics Express 7, 4621–4635 (2016).
doi: 10.1364/BOE.7.004621 pubmed: 27896001 pmcid: 5119601
Park, J. et al. Investigation of middle ear anatomy and function with combined video otoscopy-phase sensitive OCT. Biomedical Optics Express 7, 238 (2016).
doi: 10.1364/BOE.7.000238 pubmed: 26977336 pmcid: 4771445
Kim, W., Kim, S., Huang, S., Oghalai, J. S. & Applegate, B. E. Picometer scale vibrometry in the human middle ear using a surgical microscope based optical coherence tomography and vibrometry system. Biomedical Optics Express 10, 4395–4410 (2019).
doi: 10.1364/BOE.10.004395 pubmed: 31565497 pmcid: 6757470
Isensee, F., Jaeger, P. F., Kohl, S. A., Petersen, J. & Maier-Hein, K. H. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature methods 18, 203–211 (2021).
doi: 10.1038/s41592-020-01008-z pubmed: 33288961
Liu, P. et al. Non-rigid point cloud registration for middle ear diagnostics with endoscopic optical coherence tomography. International Journal of Computer Assisted Radiology and Surgery1-7 (2023).
Yang, L., Zhang, Y., Chen, J., Zhang, S. & Chen, D. Z. Suggestive annotation: A deep active learning framework for biomedical image segmentation. In Medical Image Computing and Computer Assisted Intervention- MICCAI 2017: 20th International Conference, Quebec City, QC, Canada, September 11-13, 2017, Proceedings, Part III 20, 399-407 (2017).
Bodenstedt, S. et al. Active learning using deep Bayesian networks for surgical workflow analysis. International journal of computer assisted radiology and surgery 14, 1079–1087 (2019).
doi: 10.1007/s11548-019-01963-9 pubmed: 30968355
Kirillov, A. et al. Segment Anything. Preprint at https://arxiv.org/abs/2304.02643 (2023).
Golde, J. et al. Data-informed imaging: how radiography and shape models support endoscopic OCT imaging of the middle ear. In Imaging, Therapeutics, and Advanced Technology in Head and Neck Surgery and Otolaryngology 2023, vol. 12354, 1235405 (2023).
Cuartas-Vélez, C., Restrepo, R., Bouma, B. E. & Uribe-Patarroyo, N. Volumetric non-local-means based speckle reduction for optical coherence tomography. Biomedical Optics Express 9, 3354–3372 (2018).
doi: 10.1364/BOE.9.003354 pubmed: 29984102 pmcid: 6033569
Warfield, S. K., Zou, K. H. & Wells, W. M. Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation. IEEE transactions on medical imaging 23, 903–921 (2004).
doi: 10.1109/TMI.2004.828354 pubmed: 15250643 pmcid: 1283110
Steuer, S., Golde, J., Morgenstern, J. & Liu, P. Dresden in vivo OCT Dataset of the Middle Ear (DIOME). OpARA https://doi.org/10.25532/OPARA-279 (2023).

Auteurs

Peng Liu (P)

Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Faculty of Medicine, 01307, Dresden, Germany. peng.liu@nct-dresden.de.
Department of Translational Surgical Oncology, National Center for Tumor Diseases (NCT/UCC Dresden), German Cancer Research Center (DKFZ), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307, Dresden, Germany. peng.liu@nct-dresden.de.
Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany. peng.liu@nct-dresden.de.
ORCID: 0009-0002-4280-3672

Svea Steuer (S)

Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
Clinical Sensoring and Monitoring, TUD Dresden University of Technology, 01307, Dresden, Germany.
ORCID: 0009-0002-1419-8698

Jonas Golde (J)

Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
Clinical Sensoring and Monitoring, TUD Dresden University of Technology, 01307, Dresden, Germany.
Medical Physics and Biomedical Engineering, TUD Dresden University of Technology, 01307, Dresden, Germany.
Fraunhofer Institute for Material and Beam Technology IWS, 01277, Dresden, Germany.

Joseph Morgenstern (J)

Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Faculty of Medicine, 01307, Dresden, Germany.
Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
Ear Research Center Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.
ORCID: 0000-0001-6301-9575

Yujia Hu (Y)

Department of Translational Surgical Oncology, National Center for Tumor Diseases (NCT/UCC Dresden), German Cancer Research Center (DKFZ), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307, Dresden, Germany.

Catherina Schieffer (C)

Ear Research Center Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.

Steffen Ossmann (S)

Ear Research Center Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.

Lars Kirsten (L)

Clinical Sensoring and Monitoring, TUD Dresden University of Technology, 01307, Dresden, Germany.
Medical Physics and Biomedical Engineering, TUD Dresden University of Technology, 01307, Dresden, Germany.
ORCID: 0009-0008-7642-8608

Sebastian Bodenstedt (S)

Department of Translational Surgical Oncology, National Center for Tumor Diseases (NCT/UCC Dresden), German Cancer Research Center (DKFZ), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307, Dresden, Germany.
Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
ORCID: 0000-0002-2203-9729

Micha Pfeiffer (M)

Department of Translational Surgical Oncology, National Center for Tumor Diseases (NCT/UCC Dresden), German Cancer Research Center (DKFZ), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307, Dresden, Germany.

Stefanie Speidel (S)

Department of Translational Surgical Oncology, National Center for Tumor Diseases (NCT/UCC Dresden), German Cancer Research Center (DKFZ), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307, Dresden, Germany.
Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
ORCID: 0000-0002-4590-1908

Edmund Koch (E)

Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany.
Clinical Sensoring and Monitoring, TUD Dresden University of Technology, 01307, Dresden, Germany.

Marcus Neudert (M)

Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Faculty of Medicine, 01307, Dresden, Germany. marcus.neudert@tu-dresden.de.
Else Kröner Fresenius Center, TUD Dresden University of Technology, 01307, Dresden, Germany. marcus.neudert@tu-dresden.de.
Ear Research Center Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany. marcus.neudert@tu-dresden.de.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › The Dresden in vivo OCT dataset for automatic...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › The Dresden in vivo OCT dataset for automatic...
questionsmedicales.fr › Organes des sens › Oreille › Oreille moyenne › The Dresden in vivo OCT dataset for automatic...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › Intelligence artificielle › Réseaux neuronaux (ordinateur) › The Dresden in vivo OCT dataset for automatic...
questionsmedicales.fr › Techniques d'investigation › Imagerie optique › Tomographie optique › Tomographie par cohérence optique › The Dresden in vivo OCT dataset for automatic...