Literature DB >> 33504883

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

Lena Maier-Hein1, Annette Kopp-Schneider2, Manuel Wiesenfarth3, Annika Reinke4, Bennett A Landman5, Matthias Eisenmann4, Laura Aguilera Saiz4, M Jorge Cardoso6.   

Abstract

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.

Entities:  

Year:  2021        PMID: 33504883      PMCID: PMC7841186          DOI: 10.1038/s41598-021-82017-6

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  9 in total

1.  Quantitative evaluation of software packages for single-molecule localization microscopy.

Authors:  Daniel Sage; Hagai Kirshner; Thomas Pengo; Nico Stuurman; Junhong Min; Suliana Manley; Michael Unser
Journal:  Nat Methods       Date:  2015-06-15       Impact factor: 28.547

2.  Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks.

Authors:  Oscar Jimenez-Del-Toro; Henning Muller; Markus Krenn; Katharina Gruenberg; Abdel Aziz Taha; Marianne Winterstein; Ivan Eggel; Antonio Foncubierta-Rodriguez; Orcun Goksel; Andras Jakab; Georgios Kontokotsios; Georg Langs; Bjoern H Menze; Tomas Salas Fernandez; Roger Schaer; Anna Walleyo; Marc-Andre Weber; Yashin Dicente Cid; Tobias Gass; Mattias Heinrich; Fucang Jia; Fredrik Kahl; Razmig Kechichian; Dominic Mai; Assaf B Spanier; Graham Vincent; Chunliang Wang; Daniel Wyeth; Allan Hanbury
Journal:  IEEE Trans Med Imaging       Date:  2016-06-09       Impact factor: 10.048

Review 3.  Gland segmentation in colon histology images: The glas challenge contest.

Authors:  Korsuk Sirinukunwattana; Josien P W Pluim; Hao Chen; Xiaojuan Qi; Pheng-Ann Heng; Yun Bo Guo; Li Yang Wang; Bogdan J Matuszewski; Elia Bruni; Urko Sanchez; Anton Böhm; Olaf Ronneberger; Bassem Ben Cheikh; Daniel Racoceanu; Philipp Kainz; Michael Pfeiffer; Martin Urschler; David R J Snead; Nasir M Rajpoot
Journal:  Med Image Anal       Date:  2016-09-03       Impact factor: 8.545

4.  Comparison and evaluation of methods for liver segmentation from CT datasets.

Authors:  Tobias Heimann; Bram van Ginneken; Martin A Styner; Yulia Arzhaeva; Volker Aurich; Christian Bauer; Andreas Beck; Christoph Becker; Reinhard Beichel; György Bekes; Fernando Bello; Gerd Binnig; Horst Bischof; Alexander Bornik; Peter M M Cashman; Ying Chi; Andrés Cordova; Benoit M Dawant; Márta Fidrich; Jacob D Furst; Daisuke Furukawa; Lars Grenacher; Joachim Hornegger; Dagmar Kainmüller; Richard I Kitney; Hidefumi Kobatake; Hans Lamecker; Thomas Lange; Jeongjin Lee; Brian Lennon; Rui Li; Senhu Li; Hans-Peter Meinzer; Gábor Nemeth; Daniela S Raicu; Anne-Mareike Rau; Eva M van Rikxoort; Mikaël Rousson; László Rusko; Kinda A Saddi; Günter Schmidt; Dieter Seghers; Akinobu Shimizu; Pieter Slagmolen; Erich Sorantin; Grzegorz Soza; Ruchaneewan Susomboon; Jonathan M Waite; Andreas Wimmer; Ivo Wolf
Journal:  IEEE Trans Med Imaging       Date:  2009-02-10       Impact factor: 10.048

5.  Objective comparison of particle tracking methods.

Authors:  Nicolas Chenouard; Ihor Smal; Fabrice de Chaumont; Martin Maška; Ivo F Sbalzarini; Yuanhao Gong; Janick Cardinale; Craig Carthel; Stefano Coraluppi; Mark Winter; Andrew R Cohen; William J Godinez; Karl Rohr; Yannis Kalaidzidis; Liang Liang; James Duncan; Hongying Shen; Yingke Xu; Klas E G Magnusson; Joakim Jaldén; Helen M Blau; Perrine Paul-Gilloteaux; Philippe Roudot; Charles Kervrann; François Waharte; Jean-Yves Tinevez; Spencer L Shorte; Joost Willemse; Katherine Celler; Gilles P van Wezel; Han-Wei Dan; Yuh-Show Tsai; Carlos Ortiz de Solórzano; Jean-Christophe Olivo-Marin; Erik Meijering
Journal:  Nat Methods       Date:  2014-01-19       Impact factor: 28.547

6.  An objective comparison of cell-tracking algorithms.

Authors:  Vladimír Ulman; Martin Maška; Klas E G Magnusson; Olaf Ronneberger; Carsten Haubold; Nathalie Harder; Pavel Matula; Petr Matula; David Svoboda; Miroslav Radojevic; Ihor Smal; Karl Rohr; Joakim Jaldén; Helen M Blau; Oleh Dzyubachyk; Boudewijn Lelieveldt; Pengdong Xiao; Yuexiang Li; Siu-Yeung Cho; Alexandre C Dufour; Jean-Christophe Olivo-Marin; Constantino C Reyes-Aldasoro; Jose A Solis-Lemus; Robert Bensch; Thomas Brox; Johannes Stegmaier; Ralf Mikut; Steffen Wolf; Fred A Hamprecht; Tiago Esteves; Pedro Quelhas; Ömer Demirel; Lars Malmström; Florian Jug; Pavel Tomancak; Erik Meijering; Arrate Muñoz-Barrutia; Michal Kozubek; Carlos Ortiz-de-Solorzano
Journal:  Nat Methods       Date:  2017-10-30       Impact factor: 28.547

7.  In situ click chemistry generation of cyclooxygenase-2 inhibitors.

Authors:  Atul Bhardwaj; Jatinder Kaur; Melinda Wuest; Frank Wuest
Journal:  Nat Commun       Date:  2017-02-23       Impact factor: 14.919

8.  Why rankings of biomedical image analysis competitions should be interpreted with care.

Authors:  Lena Maier-Hein; Matthias Eisenmann; Annika Reinke; Sinan Onogur; Marko Stankovic; Patrick Scholz; Tal Arbel; Hrvoje Bogunovic; Andrew P Bradley; Aaron Carass; Carolin Feldmann; Alejandro F Frangi; Peter M Full; Bram van Ginneken; Allan Hanbury; Katrin Honauer; Michal Kozubek; Bennett A Landman; Keno März; Oskar Maier; Klaus Maier-Hein; Bjoern H Menze; Henning Müller; Peter F Neher; Wiro Niessen; Nasir Rajpoot; Gregory C Sharp; Korsuk Sirinukunwattana; Stefanie Speidel; Christian Stock; Danail Stoyanov; Abdel Aziz Taha; Fons van der Sommen; Ching-Wei Wang; Marc-André Weber; Guoyan Zheng; Pierre Jannin; Annette Kopp-Schneider
Journal:  Nat Commun       Date:  2018-12-06       Impact factor: 14.919

Review 9.  The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS).

Authors:  Bjoern H Menze; Andras Jakab; Stefan Bauer; Jayashree Kalpathy-Cramer; Keyvan Farahani; Justin Kirby; Yuliya Burren; Nicole Porz; Johannes Slotboom; Roland Wiest; Levente Lanczi; Elizabeth Gerstner; Marc-André Weber; Tal Arbel; Brian B Avants; Nicholas Ayache; Patricia Buendia; D Louis Collins; Nicolas Cordier; Jason J Corso; Antonio Criminisi; Tilak Das; Hervé Delingette; Çağatay Demiralp; Christopher R Durst; Michel Dojat; Senan Doyle; Joana Festa; Florence Forbes; Ezequiel Geremia; Ben Glocker; Polina Golland; Xiaotao Guo; Andac Hamamci; Khan M Iftekharuddin; Raj Jena; Nigel M John; Ender Konukoglu; Danial Lashkari; José Antonió Mariz; Raphael Meier; Sérgio Pereira; Doina Precup; Stephen J Price; Tammy Riklin Raviv; Syed M S Reza; Michael Ryan; Duygu Sarikaya; Lawrence Schwartz; Hoo-Chang Shin; Jamie Shotton; Carlos A Silva; Nuno Sousa; Nagesh K Subbanna; Gabor Szekely; Thomas J Taylor; Owen M Thomas; Nicholas J Tustison; Gozde Unal; Flor Vasseur; Max Wintermark; Dong Hye Ye; Liang Zhao; Binsheng Zhao; Darko Zikic; Marcel Prastawa; Mauricio Reyes; Koen Van Leemput
Journal:  IEEE Trans Med Imaging       Date:  2014-12-04       Impact factor: 10.048

  9 in total
  4 in total

1.  Band selection for oxygenation estimation with multispectral/hyperspectral imaging.

Authors:  Leonardo Ayala; Fabian Isensee; Sebastian J Wirkert; Anant S Vemuri; Klaus H Maier-Hein; Baowei Fei; Lena Maier-Hein
Journal:  Biomed Opt Express       Date:  2022-02-03       Impact factor: 3.732

2.  The Medical Segmentation Decathlon.

Authors:  Michela Antonelli; Annika Reinke; Spyridon Bakas; Keyvan Farahani; Annette Kopp-Schneider; Bennett A Landman; Geert Litjens; Bjoern Menze; Olaf Ronneberger; Ronald M Summers; Bram van Ginneken; Michel Bilello; Patrick Bilic; Patrick F Christ; Richard K G Do; Marc J Gollub; Stephan H Heckers; Henkjan Huisman; William R Jarnagin; Maureen K McHugo; Sandy Napel; Jennifer S Golia Pernicka; Kawal Rhode; Catalina Tobon-Gomez; Eugene Vorontsov; James A Meakin; Sebastien Ourselin; Manuel Wiesenfarth; Pablo Arbeláez; Byeonguk Bae; Sihong Chen; Laura Daza; Jianjiang Feng; Baochun He; Fabian Isensee; Yuanfeng Ji; Fucang Jia; Ildoo Kim; Klaus Maier-Hein; Dorit Merhof; Akshay Pai; Beomhee Park; Mathias Perslev; Ramin Rezaiifar; Oliver Rippel; Ignacio Sarasua; Wei Shen; Jaemin Son; Christian Wachinger; Liansheng Wang; Yan Wang; Yingda Xia; Daguang Xu; Zhanwei Xu; Yefeng Zheng; Amber L Simpson; Lena Maier-Hein; M Jorge Cardoso
Journal:  Nat Commun       Date:  2022-07-15       Impact factor: 17.694

3.  Heidelberg colorectal data set for surgical data science in the sensor operating room.

Authors:  Lena Maier-Hein; Martin Wagner; Hannes G Kenngott; Beat P Müller-Stich; Tobias Ross; Annika Reinke; Sebastian Bodenstedt; Peter M Full; Hellena Hempe; Diana Mindroc-Filimon; Patrick Scholz; Thuy Nuong Tran; Pierangela Bruno; Anna Kisilenko; Benjamin Müller; Tornike Davitashvili; Manuela Capek; Minu D Tizabi; Matthias Eisenmann; Tim J Adler; Janek Gröhl; Melanie Schellenberg; Silvia Seidlitz; T Y Emmy Lai; Bünyamin Pekdemir; Veith Roethlingshoefer; Fabian Both; Sebastian Bittel; Marc Mengler; Lars Mündermann; Martin Apitz; Annette Kopp-Schneider; Stefanie Speidel; Felix Nickel; Pascal Probst
Journal:  Sci Data       Date:  2021-04-12       Impact factor: 6.444

4.  Semantic segmentation of multispectral photoacoustic images using deep learning.

Authors:  Melanie Schellenberg; Kris K Dreher; Niklas Holzwarth; Fabian Isensee; Annika Reinke; Nicholas Schreck; Alexander Seitel; Minu D Tizabi; Lena Maier-Hein; Janek Gröhl
Journal:  Photoacoustics       Date:  2022-03-05
  4 in total

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