Cargando…

Methods and open-source toolkit for analyzing and visualizing challenge results

Grand challenges have become the de facto standard for benchmarking image analysis algorithms. While the number of these international competitions is steadily increasing, surprisingly little effort has been invested in ensuring high quality design, execution and reporting for these international co...

Descripción completa

Detalles Bibliográficos
Autores principales: Wiesenfarth, Manuel, Reinke, Annika, Landman, Bennett A., Eisenmann, Matthias, Saiz, Laura Aguilera, Cardoso, M. Jorge, Maier-Hein, Lena, Kopp-Schneider, Annette
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841186/
https://www.ncbi.nlm.nih.gov/pubmed/33504883
http://dx.doi.org/10.1038/s41598-021-82017-6
_version_ 1783643749160583168
author Wiesenfarth, Manuel
Reinke, Annika
Landman, Bennett A.
Eisenmann, Matthias
Saiz, Laura Aguilera
Cardoso, M. Jorge
Maier-Hein, Lena
Kopp-Schneider, Annette
author_facet Wiesenfarth, Manuel
Reinke, Annika
Landman, Bennett A.
Eisenmann, Matthias
Saiz, Laura Aguilera
Cardoso, M. Jorge
Maier-Hein, Lena
Kopp-Schneider, Annette
author_sort Wiesenfarth, Manuel
collection PubMed
description Grand challenges have become the de facto standard for benchmarking image analysis algorithms. While the number of these international competitions is steadily increasing, surprisingly little effort has been invested in ensuring high quality design, execution and reporting for these international competitions. Specifically, results analysis and visualization in the event of uncertainties have been given almost no attention in the literature. Given these shortcomings, the contribution of this paper is two-fold: (1) we present a set of methods to comprehensively analyze and visualize the results of single-task and multi-task challenges and apply them to a number of simulated and real-life challenges to demonstrate their specific strengths and weaknesses; (2) we release the open-source framework challengeR as part of this work to enable fast and wide adoption of the methodology proposed in this paper. Our approach offers an intuitive way to gain important insights into the relative and absolute performance of algorithms, which cannot be revealed by commonly applied visualization techniques. This is demonstrated by the experiments performed in the specific context of biomedical image analysis challenges. Our framework could thus become an important tool for analyzing and visualizing challenge results in the field of biomedical image analysis and beyond.
format Online
Article
Text
id pubmed-7841186
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-78411862021-01-29 Methods and open-source toolkit for analyzing and visualizing challenge results Wiesenfarth, Manuel Reinke, Annika Landman, Bennett A. Eisenmann, Matthias Saiz, Laura Aguilera Cardoso, M. Jorge Maier-Hein, Lena Kopp-Schneider, Annette Sci Rep Article Grand challenges have become the de facto standard for benchmarking image analysis algorithms. While the number of these international competitions is steadily increasing, surprisingly little effort has been invested in ensuring high quality design, execution and reporting for these international competitions. Specifically, results analysis and visualization in the event of uncertainties have been given almost no attention in the literature. Given these shortcomings, the contribution of this paper is two-fold: (1) we present a set of methods to comprehensively analyze and visualize the results of single-task and multi-task challenges and apply them to a number of simulated and real-life challenges to demonstrate their specific strengths and weaknesses; (2) we release the open-source framework challengeR as part of this work to enable fast and wide adoption of the methodology proposed in this paper. Our approach offers an intuitive way to gain important insights into the relative and absolute performance of algorithms, which cannot be revealed by commonly applied visualization techniques. This is demonstrated by the experiments performed in the specific context of biomedical image analysis challenges. Our framework could thus become an important tool for analyzing and visualizing challenge results in the field of biomedical image analysis and beyond. Nature Publishing Group UK 2021-01-27 /pmc/articles/PMC7841186/ /pubmed/33504883 http://dx.doi.org/10.1038/s41598-021-82017-6 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Wiesenfarth, Manuel
Reinke, Annika
Landman, Bennett A.
Eisenmann, Matthias
Saiz, Laura Aguilera
Cardoso, M. Jorge
Maier-Hein, Lena
Kopp-Schneider, Annette
Methods and open-source toolkit for analyzing and visualizing challenge results
title Methods and open-source toolkit for analyzing and visualizing challenge results
title_full Methods and open-source toolkit for analyzing and visualizing challenge results
title_fullStr Methods and open-source toolkit for analyzing and visualizing challenge results
title_full_unstemmed Methods and open-source toolkit for analyzing and visualizing challenge results
title_short Methods and open-source toolkit for analyzing and visualizing challenge results
title_sort methods and open-source toolkit for analyzing and visualizing challenge results
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841186/
https://www.ncbi.nlm.nih.gov/pubmed/33504883
http://dx.doi.org/10.1038/s41598-021-82017-6
work_keys_str_mv AT wiesenfarthmanuel methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT reinkeannika methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT landmanbennetta methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT eisenmannmatthias methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT saizlauraaguilera methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT cardosomjorge methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT maierheinlena methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults
AT koppschneiderannette methodsandopensourcetoolkitforanalyzingandvisualizingchallengeresults