Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease.
application programming interface
data integration
data publication and archiving
diabetes
human pancreas development
imaging databases
microscopy
open source
pancreas imaging
software
web resource
Journal
Patterns (New York, N.Y.)
ISSN: 2666-3899
Titre abrégé: Patterns (N Y)
Pays: United States
ID NLM: 101767765
Informations de publication
Date de publication:
13 Nov 2020
13 Nov 2020
Historique:
received:
19
03
2020
revised:
31
08
2020
accepted:
14
09
2020
entrez:
9
12
2020
pubmed:
10
12
2020
medline:
10
12
2020
Statut:
epublish
Résumé
Human tissue phenotyping generates complex spatial information from numerous imaging modalities, yet images typically become static figures for publication, and original data and metadata are rarely available. While comprehensive image maps exist for some organs, most resources have limited support for multiplexed imaging or have non-intuitive user interfaces. Therefore, we built a Pancreatlas resource that integrates several technologies into a unique interface, allowing users to access richly annotated web pages, drill down to individual images, and deeply explore data online. The current version of Pancreatlas contains over 800 unique images acquired by whole-slide scanning, confocal microscopy, and imaging mass cytometry, and is available at https://www.pancreatlas.org. To create this human pancreas-specific biological imaging resource, we developed a React-based web application and Python-based application programming interface, collectively called Flexible Framework for Integrating and Navigating Data (FFIND), which can be adapted beyond Pancreatlas to meet countless imaging or other structured data-management needs.
Identifiants
pubmed: 33294866
doi: 10.1016/j.patter.2020.100120
pii: S2666-3899(20)30161-6
pmc: PMC7691395
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100120Informations de copyright
© 2020 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
Diabetologia. 2020 Jul;63(7):1418-1423
pubmed: 32388592
Nature. 2019 Oct;574(7777):187-192
pubmed: 31597973
Diabetes Care. 2017 May;40(5):723-725
pubmed: 28428323
PLoS Comput Biol. 2019 May 16;15(5):e1006958
pubmed: 31095554
Islets. 2019;11(2):44-49
pubmed: 31084520
Nat Methods. 2016 May;13(5):387-8
pubmed: 27067018
Trends Biochem Sci. 2002 Nov;27(11):589
pubmed: 12417136
Bioinformatics. 2010 Apr 15;26(8):1112-8
pubmed: 20200009
PLoS One. 2016 Apr 29;11(4):e0154556
pubmed: 27128319
J Am Soc Nephrol. 2008 Apr;19(4):667-71
pubmed: 18287559
Nat Methods. 2018 Nov;15(11):849-854
pubmed: 30377375
Am J Physiol Lung Cell Mol Physiol. 2017 Nov 1;313(5):L733-L740
pubmed: 28798251
Diabetes. 2019 Jul;68(7):1394-1402
pubmed: 31127054
Bioinformatics. 2016 Nov 15;32(22):3471-3479
pubmed: 27412095
Immunogenetics. 2020 Feb;72(1-2):57-76
pubmed: 31761977
Cell Metab. 2019 Mar 5;29(3):769-783.e4
pubmed: 30713110
Cell. 2018 Aug 9;174(4):968-981.e15
pubmed: 30078711
Acta Crystallogr D Struct Biol. 2017 Jun 01;73(Pt 6):503-508
pubmed: 28580912
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
BMC Genomics. 2019 Jan 5;20(1):6
pubmed: 30611200
Bioinformatics. 2017 Jul 15;33(14):2218-2220
pubmed: 28369191
Mamm Genome. 2015 Oct;26(9-10):441-7
pubmed: 26223880
Nature. 2012 Sep 20;489(7416):391-399
pubmed: 22996553
Nat Methods. 2017 Aug;14(8):775-781
pubmed: 28775673
Nature. 2014 Apr 10;508(7495):199-206
pubmed: 24695229
Front Genet. 2012 May 28;3:87
pubmed: 22654893
JCI Insight. 2018 Apr 19;3(8):
pubmed: 29669939
Nat Methods. 2012 Feb 28;9(3):245-53
pubmed: 22373911
Development. 2011 Jul;138(13):2845-53
pubmed: 21652655
Diabetes. 2019 Jul;68(7):1363-1365
pubmed: 31092479
J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8
pubmed: 21550421
J Cell Biol. 2010 May 31;189(5):777-82
pubmed: 20513764
J Histochem Cytochem. 2019 Jan;67(1):41-52
pubmed: 29771178
Nucleic Acids Res. 2020 Jan 8;48(D1):D1-D8
pubmed: 31906604