PyHIST: A Histological Image Segmentation Tool
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Muñoz-Aguirre, Manuel
- dc.contributor.author Ntasis, Vasilis F.
- dc.contributor.author Rojas, Santiago
- dc.contributor.author Guigó Serra, Roderic
- dc.date.accessioned 2020-11-17T06:54:43Z
- dc.date.available 2020-11-17T06:54:43Z
- dc.date.issued 2020
- dc.description.abstract The development of increasingly sophisticated methods to acquire high-resolution images has led to the generation of large collections of biomedical imaging data, including images of tissues and organs. Many of the current machine learning methods that aim to extract biological knowledge from histopathological images require several data preprocessing stages, creating an overhead before the proper analysis. Here we present PyHIST (https://github.com/manuel-munoz-aguirre/PyHIST), an easy-to-use, open source whole slide histological image tissue segmentation and preprocessing command-line tool aimed at tile generation for machine learning applications. From a given input image, the PyHIST pipeline i) optionally rescales the image to a different resolution, ii) produces a mask for the input image which separates the background from the tissue, and iii) generates individual image tiles with tissue content.
- dc.description.sponsorship The authors received no specific funding for this work. M.M.-A. performs his research with support of pre-doctoral fellowship FPU15/03635 from Ministerio de Educación, Cultura y Deporte. (URL: http://www.mecd.gob.es/) Agencia Estatal de Investigación (AEI) and FEDER under project PGC2018-094017-B-I00 is also acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- dc.format.mimetype application/pdf
- dc.identifier.citation Muñoz-Aguirre M, Ntasis VF, Rojas S, Guigó R. PyHIST: A Histological Image Segmentation Tool. PLoS Comput Biol. 2020; 16(10):e1008349. DOI: 10.1371/journal.pcbi.1008349
- dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1008349
- dc.identifier.issn 1553-734X
- dc.identifier.uri http://hdl.handle.net/10230/45782
- dc.language.iso eng
- dc.publisher Public Library of Science (PLoS)
- dc.relation.ispartof PLoS Comput Biol. 2020; 16(10):e1008349
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-094017-B-I00
- dc.rights © 2020 Muñoz-Aguirre 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.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Hepatocellular carcinoma
- dc.subject.keyword Preprocessing
- dc.subject.keyword Histology
- dc.subject.keyword Breast cancer
- dc.subject.keyword Imaging techniques
- dc.subject.keyword Machine learning
- dc.subject.keyword Cancer detection and diagnosis
- dc.subject.keyword Deep learning
- dc.title PyHIST: A Histological Image Segmentation Tool
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion