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http://hdl.handle.net/1942/44408
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DC Field | Value | Language |
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dc.contributor.author | GEUBBELMANS, Melvin | - |
dc.contributor.author | CLAES, Jari | - |
dc.contributor.author | NIJSTEN, Kim | - |
dc.contributor.author | GERVOIS, Pascal | - |
dc.contributor.author | APPELTANS, Simon | - |
dc.contributor.author | MARTENS, Sandrina | - |
dc.contributor.author | WOLFS, Esther | - |
dc.contributor.author | THOMEER, Michiel | - |
dc.contributor.author | VALKENBORG, Dirk | - |
dc.contributor.author | FAES, Christel | - |
dc.contributor.editor | Zhang, Xiaohui | - |
dc.date.accessioned | 2024-10-02T08:33:55Z | - |
dc.date.available | 2024-10-02T08:33:55Z | - |
dc.date.issued | 2024 | - |
dc.date.submitted | 2024-09-20T14:07:30Z | - |
dc.identifier.citation | Plos One, 19 (9) (Art N° e0309740) | - |
dc.identifier.uri | http://hdl.handle.net/1942/44408 | - |
dc.description.abstract | Digital pathology has become increasingly popular for research and clinical applications. Using high-quality microscopes to produce Whole Slide Images of tumor tissue enables the discovery of insights into biological aspects invisible to the human eye. These are acquired through downstream analyses using spatial statistics and artificial intelligence. Determination of the quality and consistency of these images is needed to ensure accurate outcomes when identifying clinical and subclinical image features. Additionally, the time-intensive process of generating high-volume images results in a trade-off that needs to be carefully balanced. This study aims to determine optimal instrument settings to generate representative images of pathological tissue using digital microscopy. Using various settings, an H&E stained sample was scanned using the ZEISS Axio Scan.Z1. Next, nucleus segmentation was performed on resulting images using StarDist. Subsequently, detections were compared between scans using a matching algorithm. Finally, nucleus-level information was compared between scans. Results indicated that while general matching percentages were high, similarity between information from replicates was relatively low. Additionally, settings resulting in longer scanning times and increased data volume did not increase similarity between replicates. In conclusion, the scan setting ultimately deemed optimal combined consistent and qualitative performance with low throughput time. | - |
dc.description.sponsorship | Funding All authors gratefully acknowledge funding by Bijzonder Onderzoeksfonds UHasselt (project "Future proof pathology for predictive medicine and disease prognosis based on tumor heterogeneity", project number R-11405), as well as funding by the Flemish Government under the Onderzoeksprogramma Artificie¨le Intelligentie (AI) Vlaanderen program (https://www. flandersairesearch.be/en). The sponsors or funders did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We would like to thank The Cancer Genome Atlas (TCGA), as the StarDist algorithm used in our analyses was trained on the MoNuSeg 2018 dataset, which uses annotated data extracted from TCGA. | - |
dc.language.iso | en | - |
dc.publisher | PUBLIC LIBRARY SCIENCE | - |
dc.rights | 2024 Geubbelmans et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | - |
dc.subject.other | Humans | - |
dc.subject.other | Image Processing, Computer-Assisted | - |
dc.subject.other | Algorithms | - |
dc.subject.other | Microscopy | - |
dc.subject.other | Cell Nucleus | - |
dc.subject.other | Lung Neoplasms | - |
dc.title | Optimization of whole slide imaging scan settings for computer vision using human lung cancer tissue | - |
dc.type | Journal Contribution | - |
dc.identifier.issue | 9 | - |
dc.identifier.volume | 19 | - |
local.format.pages | 15 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | Valkenborg, D; Faes, C (corresponding author), Hasselt Univ, Data Sci Inst, Hasselt, Belgium. | - |
dc.description.notes | dirk.valkenborg@uhasselt.be; christel.faes@uhasselt.be | - |
local.publisher.place | 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
local.bibliographicCitation.artnr | e0309740 | - |
dc.identifier.doi | 10.1371/journal.pone.0309740 | - |
dc.identifier.pmid | 39250489 | - |
dc.identifier.isi | 001309221100009 | - |
dc.contributor.orcid | NIJSTEN, Kim/0000-0001-8085-8311 | - |
dc.identifier.eissn | - | |
local.provider.type | wosris | - |
local.description.affiliation | [Geubbelmans, Melvin; Claes, Jari; Appeltans, Simon; Valkenborg, Dirk; Faes, Christel] Hasselt Univ, Data Sci Inst, Hasselt, Belgium. | - |
local.description.affiliation | [Nijsten, Kim; Gervois, Pascal; Martens, Sandrina; Wolfs, Esther] UHasselt, Lab Funct Imaging & Res Stem Cells, FIERCE Lab, BIOMED, Diepenbeek, Belgium. | - |
local.description.affiliation | [Gervois, Pascal; Thomeer, Michiel] UHasselt, Limburg Clin Res Ctr LCRC, Hasselt, Belgium. | - |
local.description.affiliation | [Thomeer, Michiel] Ziekenhuis Oost Limburg, Dept Resp Med, Genk, Belgium. | - |
local.uhasselt.international | no | - |
item.accessRights | Open Access | - |
item.contributor | GEUBBELMANS, Melvin | - |
item.contributor | CLAES, Jari | - |
item.contributor | NIJSTEN, Kim | - |
item.contributor | GERVOIS, Pascal | - |
item.contributor | APPELTANS, Simon | - |
item.contributor | MARTENS, Sandrina | - |
item.contributor | WOLFS, Esther | - |
item.contributor | THOMEER, Michiel | - |
item.contributor | VALKENBORG, Dirk | - |
item.contributor | FAES, Christel | - |
item.contributor | Zhang, Xiaohui | - |
item.fullcitation | GEUBBELMANS, Melvin; CLAES, Jari; NIJSTEN, Kim; GERVOIS, Pascal; APPELTANS, Simon; MARTENS, Sandrina; WOLFS, Esther; THOMEER, Michiel; VALKENBORG, Dirk & FAES, Christel (2024) Optimization of whole slide imaging scan settings for computer vision using human lung cancer tissue. In: Plos One, 19 (9) (Art N° e0309740). | - |
item.fulltext | With Fulltext | - |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
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journal.pone.0309740.pdf | Published version | 1.77 MB | Adobe PDF | View/Open |
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