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Democratized image analytics by visual programming through integration of deep models and small-scale machine learning
Godec, Primož (Author), Pančur, Matjaž (Author), Ilenič, Nejc (Author), Čopar, Andrej (Author), Stražar, Martin (Author), Erjavec, Aleš (Author), Pretnar, Ajda (Author), Demšar, Janez (Author), Starič, Anže (Author), Toplak, Marko (Author), Žagar, Lan (Author), Hartman, Jan (Author), Hamilton, Wang (Author), Bellazzi, Riccardo (Author), Petrovič, Uroš (Author), Garagna, Silvia (Author), Zuccotti, Maurizio (Author), Park, Dongsu (Author), Shaulsky, Gad (Author), Zupan, Blaž (Author)

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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)
Tipology:1.01 - Original Scientific Article
Organization:FRI - Faculty of computer and information science
Year:2019
Number of pages:Str. 1-7
Numbering:Vol. 10, art. 4551
UDC:004.9:577
ISSN on article:2041-1723
DOI:10.1038/s41467-019-12397-x This link opens in a new window
COBISS.SI-ID:32755751 This link opens in a new window
Views:79
Downloads:54
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Record is a part of a journal

Title:Nature communications
Publisher:Springer Nature
ISSN:2041-1723
COBISS.SI-ID:2315876 This link opens in a new window

Document is financed by a project

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project no.:P2-0209
Name:Umetna inteligenca in inteligentni sistemi

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project no.:BI-US/17-18-014
Name:

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project no.:P1-0207
Name:Toksini in biomembrane

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Project no.:N1-0034
Name:Medsebojni vpliv med lipidnim in osrednjim ogljikovim metabolizmom

Funder:NIH - National Institutes of Health
Project no.:R35 GM118016
Name:

Funder:NIH - National Institutes of Health
Funding Programme:National Institute of Arthritis and Musculoskeletal and Skin Diseases
Project no.:R01AR072018
Name:

Funder:Drugi - Drug financer ali več financerjev
Funding Programme:Italian Ministry of Education, University and Research
Project no.:
Name:Dipartimenti di Eccelenza Program (2018-2022)

Funder:Drugi - Drug financer ali več financerjev
Funding Programme:Fondazione Regionale per la Ricerca Biomedica
Project no.:2015-0042
Name:

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

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