The Image Data Explorer: Interactive exploration of image-derived data.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2022
2022
Historique:
received:
13
05
2022
accepted:
12
08
2022
entrez:
15
9
2022
pubmed:
16
9
2022
medline:
20
9
2022
Statut:
epublish
Résumé
Many bioimage analysis projects produce quantitative descriptors of regions of interest in images. Associating these descriptors with visual characteristics of the objects they describe is a key step in understanding the data at hand. However, as many bioimage data and their analysis workflows are moving to the cloud, addressing interactive data exploration in remote environments has become a pressing issue. To address it, we developed the Image Data Explorer (IDE) as a web application that integrates interactive linked visualization of images and derived data points with exploratory data analysis methods, annotation, classification and feature selection functionalities. The IDE is written in R using the shiny framework. It can be easily deployed on a remote server or on a local computer. The IDE is available at https://git.embl.de/heriche/image-data-explorer and a cloud deployment is accessible at https://shiny-portal.embl.de/shinyapps/app/01_image-data-explorer.
Identifiants
pubmed: 36107835
doi: 10.1371/journal.pone.0273698
pii: PONE-D-22-14030
pmc: PMC9477257
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0273698Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Nat Methods. 2018 Nov;15(11):849-854
pubmed: 30377375
BMC Bioinformatics. 2017 Nov 29;18(1):529
pubmed: 29187165
J Biomol Screen. 2012 Apr;17(4):496-506
pubmed: 22233649
Mol Biol Cell. 2014 Aug 15;25(16):2522-36
pubmed: 24943848
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
Nat Methods. 2017 Aug;14(8):775-781
pubmed: 28775673
J Cell Sci. 2019 Nov 21;132(22):
pubmed: 31754043
Bioinformatics. 2021 Sep 03;:
pubmed: 34478488
Cell Syst. 2018 Jun 27;6(6):636-653
pubmed: 29953863
Nature. 2016 Jun 29;535(7611):308-12
pubmed: 27362226
Bioinformatics. 2010 Apr 1;26(7):979-81
pubmed: 20338898
J Cell Sci. 2013 Dec 15;126(Pt 24):5529-39
pubmed: 24259662
Nat Methods. 2021 Dec;18(12):1496-1498
pubmed: 34845388
J Cell Biol. 2010 May 31;189(5):777-82
pubmed: 20513764
J Cell Biol. 2001 May 28;153(5):1097-110
pubmed: 11381093
J Biol Chem. 2014 Dec 12;289(50):34601-19
pubmed: 25349213