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WSIC : a Python package and command-line interface for fast whole slide image conversion
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Pocock, Johnathan, Raza, Shan-e-Ahmed, Minhas, Fayyaz ul Amir Afsar and Rajpoot, Nasir M. (Nasir Mahmood) (2023) WSIC : a Python package and command-line interface for fast whole slide image conversion. Bioinformatics Advances, 3 (1). vbad122. doi:10.1093/bioadv/vbad122 ISSN 2635-0041.
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WRAP-WSIC-Python-package-command-line-interface-fast-whole-slide-image-conversion-2023.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (483Kb) | Preview |
Official URL: https://doi.org/10.1093/bioadv/vbad122
Abstract
Summary: Whole slide images (WSIs) are multi-gigapixel images of tissue sections, which are used in digital and computational pathology workflows. WSI datasets are commonly heterogeneous collections of proprietary or niche specialized formats which are challenging to handle. This note describes an open-source Python application for efficiently converting between WSI formats, including common, open, and emerging cloud-friendly formats. WSIC is a software tool that can quickly convert WSI files across various formats. It has a high performance and maintains the resolution metadata of the original images. WSIC is ideal for pre-processing large-scale WSI datasets with different file types.
Availability and implementation: Source code is available on GitHub at https://github.com/John-P/wsic/ under a permissive licence. WSIC is also available as a package on PyPI at https://pypi.org/project/WSIC/.
Item Type: | Journal Article | ||||||
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Subjects: | Q Science > QA Mathematics > QA75 (Please use QA76 Electronic Computers. Computer Science) R Medicine > RC Internal medicine |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | ||||||
SWORD Depositor: | Library Publications Router | ||||||
Library of Congress Subject Headings (LCSH): | Diagnostic imaging -- Digital techniques, Python (Computer program language) | ||||||
Journal or Publication Title: | Bioinformatics Advances | ||||||
Publisher: | Oxford University Press (OUP) | ||||||
ISSN: | 2635-0041 | ||||||
Official Date: | 9 September 2023 | ||||||
Dates: |
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Volume: | 3 | ||||||
Number: | 1 | ||||||
Article Number: | vbad122 | ||||||
DOI: | 10.1093/bioadv/vbad122 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 2 October 2023 | ||||||
Date of first compliant Open Access: | 2 October 2023 | ||||||
RIOXX Funder/Project Grant: |
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