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DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners

The evolution of biomedical imaging technology is allowing the digitization of hundreds of glass slides at once. There are multiple microscope scanners available in the market including low-cost solutions that can serve small centers. Moreover, new technology is being researched to acquire images an...

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Detalles Bibliográficos
Autores principales: Gupta, Yubraj, Costa, Carlos, Pinho, Eduardo, Bastião Silva, Luís
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954093/
https://www.ncbi.nlm.nih.gov/pubmed/35336492
http://dx.doi.org/10.3390/s22062322
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author Gupta, Yubraj
Costa, Carlos
Pinho, Eduardo
Bastião Silva, Luís
author_facet Gupta, Yubraj
Costa, Carlos
Pinho, Eduardo
Bastião Silva, Luís
author_sort Gupta, Yubraj
collection PubMed
description The evolution of biomedical imaging technology is allowing the digitization of hundreds of glass slides at once. There are multiple microscope scanners available in the market including low-cost solutions that can serve small centers. Moreover, new technology is being researched to acquire images and new modalities are appearing in the market such as electron microscopy. This reality offers new diagnostics tools to clinical practice but emphasizes also the lack of multivendor system’s interoperability. Without the adoption of standard data formats and communications methods, it will be impossible to build this industry through the installation of vendor-neutral archives and the establishment of telepathology services in the cloud. The DICOM protocol is a feasible solution to the aforementioned problem because it already provides an interface for visible light and whole slide microscope imaging modalities. While some scanners currently have DICOM interfaces, the vast majority of manufacturers continue to use proprietary solutions. This article proposes an automated DICOMization pipeline that can efficiently transform distinct proprietary microscope images from CLSM, FIB-SEM, and WSI scanners into standard DICOM with their biological information maintained within their metadata. The system feasibility and performance were evaluated with fifteen distinct proprietary modalities, including stacked WSI samples. The results demonstrated that the proposed methodology is accurate and can be used in production. The normalized objects were stored through the standard communications in the Dicoogle open-source archive.
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spelling pubmed-89540932022-03-26 DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners Gupta, Yubraj Costa, Carlos Pinho, Eduardo Bastião Silva, Luís Sensors (Basel) Article The evolution of biomedical imaging technology is allowing the digitization of hundreds of glass slides at once. There are multiple microscope scanners available in the market including low-cost solutions that can serve small centers. Moreover, new technology is being researched to acquire images and new modalities are appearing in the market such as electron microscopy. This reality offers new diagnostics tools to clinical practice but emphasizes also the lack of multivendor system’s interoperability. Without the adoption of standard data formats and communications methods, it will be impossible to build this industry through the installation of vendor-neutral archives and the establishment of telepathology services in the cloud. The DICOM protocol is a feasible solution to the aforementioned problem because it already provides an interface for visible light and whole slide microscope imaging modalities. While some scanners currently have DICOM interfaces, the vast majority of manufacturers continue to use proprietary solutions. This article proposes an automated DICOMization pipeline that can efficiently transform distinct proprietary microscope images from CLSM, FIB-SEM, and WSI scanners into standard DICOM with their biological information maintained within their metadata. The system feasibility and performance were evaluated with fifteen distinct proprietary modalities, including stacked WSI samples. The results demonstrated that the proposed methodology is accurate and can be used in production. The normalized objects were stored through the standard communications in the Dicoogle open-source archive. MDPI 2022-03-17 /pmc/articles/PMC8954093/ /pubmed/35336492 http://dx.doi.org/10.3390/s22062322 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gupta, Yubraj
Costa, Carlos
Pinho, Eduardo
Bastião Silva, Luís
DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title_full DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title_fullStr DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title_full_unstemmed DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title_short DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners
title_sort dicomization of proprietary files obtained from confocal, whole-slide, and fib-sem microscope scanners
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954093/
https://www.ncbi.nlm.nih.gov/pubmed/35336492
http://dx.doi.org/10.3390/s22062322
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