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Democratized image analytics by visual programming through integration of deep models and small-scale machine learning
ID
Godec, Primož
(
Author
),
ID
Pančur, Matjaž
(
Author
),
ID
Ilenič, Nejc
(
Author
),
ID
Čopar, Andrej
(
Author
),
ID
Stražar, Martin
(
Author
),
ID
Erjavec, Aleš
(
Author
),
ID
Pretnar, Ajda
(
Author
),
ID
Demšar, Janez
(
Author
),
ID
Starič, Anže
(
Author
),
ID
Toplak, Marko
(
Author
),
ID
Žagar, Lan
(
Author
),
ID
Hartman, Jan
(
Author
),
ID
Hamilton, Wang
(
Author
),
ID
Bellazzi, Riccardo
(
Author
),
ID
Petrovič, Uroš
(
Author
),
ID
Garagna, Silvia
(
Author
),
ID
Zuccotti, Maurizio
(
Author
),
ID
Park, Dongsu
(
Author
),
ID
Shaulsky, Gad
(
Author
),
ID
Zupan, Blaž
(
Author
)
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URL - Source URL, Visit
https://www.nature.com/articles/s41467-019-12397-x
Abstract
Analysis of biomedical images requires computational expertize that are uncommon among biomedical scientists. Deep learning approaches for image analysis provide an opportunity to develop user-friendly tools for exploratory data analysis. Here, we use the visual programming toolbox Orange (http://orange.biolab.si) to simplify image analysis by integrating deep-learning embedding, machine learning procedures, and data visualization. Orange supports the construction of data analysis workflows by assembling components for data preprocessing, visualization, and modeling. We equipped Orange with components that use pre-trained deep convolutional networks to profile images with vectors of features. These vectors are used in image clustering and classification in a framework that enables mining of image sets for both novel and experienced users. We demonstrate the utility of the tool in image analysis of progenitor cells in mouse bone healing, identification of developmental competence in mouse oocytes, subcellular protein localization in yeast, and developmental morphology of social amoebae.
Language:
English
Keywords:
algorithm
,
biochemical composition
,
data assimilation
,
data mining
,
image analysis
,
machine learning
,
numerical model
,
protein
,
visualization
Work type:
Article (dk_c)
Typology:
1.01 - Original Scientific Article
Organization:
FRI - Faculty of computer and information science
BF - Biotechnical Faculty
Year:
2019
Publication status in journal:
Published
Article version:
Publisher's version of article
Number of pages:
7 str.
Numbering:
Vol. 10, art. 4551
UDC:
004.9:577
ISSN on article:
2041-1723
DOI:
10.1038/s41467-019-12397-x
COBISS.SI-ID:
32755751
Publication date in RUL:
25.03.2021
Views:
402
Downloads:
184
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Record is a part of a journal
Title:
Nature communications
Publisher:
Springer Nature
ISSN:
2041-1723
COBISS.SI-ID:
2315876
Licences
License:
CC BY 4.0, Creative Commons Attribution 4.0 International
Link:
http://creativecommons.org/licenses/by/4.0/
Description:
This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:
25.03.2021
Document is financed by a project
Funder:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project number:
P2-0209
Name:
Umetna inteligenca in inteligentni sistemi
Funder:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project number:
BI-US/17-18-014
Funder:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project number:
P1-0207
Name:
Toksini in biomembrane
Funder:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project number:
N1-0034
Name:
Medsebojni vpliv med lipidnim in osrednjim ogljikovim metabolizmom
Funder:
NIH - National Institutes of Health
Project number:
R35 GM118016
Funder:
NIH - National Institutes of Health
Funding programme:
National Institute of Arthritis and Musculoskeletal and Skin Diseases
Project number:
R01AR072018
Funder:
Drugi - Drug financer ali več financerjev
Funding programme:
Italian Ministry of Education, University and Research
Name:
Dipartimenti di Eccelenza Program (2018-2022)
Funder:
Drugi - Drug financer ali več financerjev
Funding programme:
Fondazione Regionale per la Ricerca Biomedica
Project number:
2015-0042
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