TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning
TLDR
Support for 2D, 3D and 4D images such as X-ray, histopathology, CT, ultrasound and diffusion MRI and focus on reproducibility and traceability to encourage open-science practices.About:
This article is published in Computer Methods and Programs in Biomedicine.The article was published on 2021-06-17 and is currently open access. It has received 292 citations till now. The article focuses on the topics: Image processing & Python (programming language).read more
Citations
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Journal ArticleDOI
A review of medical image data augmentation techniques for deep learning applications.
Phillip Chlap,Phillip Chlap,Hang Min,Hang Min,Nym Vandenberg,Jason Dowling,Jason Dowling,Lois Holloway,Annette Haworth +8 more
TL;DR: Data augmentation aims to generate additional data which is used to train the model and has been shown to improve performance when validated on a separate unseen dataset as discussed by the authors, which has become a popular method for increasing the size of a training dataset, particularly in fields where large datasets aren't typically available.
Journal ArticleDOI
Federated learning enables big data for rare cancer boundary detection
Sarthak Pati,Ujjwal Baid,Brandon Edwards,Micah J. Sheller,Shih-han Wang,G. Anthony Reina,Patrick Foley,Alexey Gruzdev,Deepthi Karkada,Christos Davatzikos,Chiharu Sako,Satyam Ghodasara,Michel Bilello,Suyash Mohan,Philipp Vollmuth,Gianluca Brugnara,Chandrakanth Jayachandran Preetha,Felix Sahm,Klaus H. Maier-Hein,Maximilian Zenk,Martin Bendszus,Wolfgang Wick,R. Calabrese,Jeffrey D. Rudie,Javier Villanueva-Meyer,So Yeon Cha,Madhura Ingalhalikar,Manali Jadhav,Umang Pandey,Jitender Saini,John Garrett,Matthew H. Larson,Robert Jeraj,Stuart Currie,R. Frood,Kavi Fatania,Raymond Y. Huang,Ken Chang,Carmen Balaña Quintero,Jaume Capellades,Josep Puig,Johannes Trenkler,Josef Pichler,Georg Necker,Andreas Haunschmidt,Stephan Meckel,Gaurav Shukla,Spencer Liem,Gregory S. Alexander,Joseph Lombardo,Joshua D. Palmer,Adam E. Flanders,Adam P. Dicker,Haris I. Sair,Craig K. Jones,Archana Venkataraman,Meirui Jiang,Tiffany Y. So,Cheng Chen,Pheng-Ann Heng,Qi Dou,Michal Kozubek,Filip Lux,Jan Mich'alek,Petr Matula,Milovs Kevrkovsk'y,Tereza Kopvrivov'a,Marek Dost'al,V'aclav Vyb'ihal,Michael A. Vogelbaum,James R. Mitchell,Joaquim M. Farinhas,Joseph A. Maldjian,Chandan Ganesh Bangalore Yogananda,Marco Da Cunha Pinho,Divya madhuri Reddy,James M. Holcomb,Benjamin C. Wagner,Benjamin M. Ellingson,Timothy F. Cloughesy,Catalina Raymond,Talia Oughourlian,Akifumi Hagiwara,Chencai Wang,Minh-Son To,Sargam Bhardwaj,Chee Chong,Marc Agzarian,Alexandre X. Falcão,Samuel Botter Martins,Bernardo Teixeira,Flávia Sprenger,David Menotti,Diego R. Lucio,Pamela LaMontagne,Daniel S. Marcus,Benedikt Wiestler,Florian Kofler,Ivan Ezhov,Marie-Christin Metz,Rajan B. Jain,Matthew C. H. Lee,Yvonne W. Lui,Richard McKinley,Johannes Slotboom,Piotr Radojewski,Raphael Meier,Roland Wiest,Derrick Murcia,Eric Fu,Rourke Haas,Johnna Kellie Fox Thompson,D. Ryan Ormond,Chaitra Badve,Andrew E. Sloan,Vachan Vadmal,Kristin Waite,Rivka R. Colen,Linmin Pei,Murat Ak,Ashok Srinivasan,J. Rajiv Bapuraj,Arvind Rao,Nicholas C. Wang,Ota Yoshiaki,Toshio Moritani,Sevcan Turk,Joonsang Lee,Snehal Prabhudesai,Fanny Mor'on,Jacob Mandel,Konstantinos Kamnitsas,Ben Glocker,Luke Dixon,Matthew Ian Williams,Peter Zampakis,V. Panagiotopoulos,Panagiotis Tsiganos,Sotiris Alexiou,Ilias Haliassos,Evangelia I. Zacharaki,Konstantinos Moustakas,Christina Kalogeropoulou,Dimitrios Kardamakis,Yoon Seong Choi,Seung Koo Lee,Jong Hee Chang,Sung Soo Ahn,Bing Luo,Laila M. Poisson,Ning Wen,Pallavi Tiwari,Ruchika Verma,Rohan Bareja,Ipsa Yadav,Jonathan Chen,Neeraj Kumar,Marion Smits,Sebastian R. van der Voort,Ahmed Alafandi,Fatih Incekara,Maarten M. J. Wijnenga,Georgios Kapas,Renske Gahrmann,Joost Schouten,Hendrikus J. Dubbink,Arnaud J P E Vincent,Martin J. van den Bent,Pim J. French,Stefan Halle Klein,Yading Yuan,Sonam Sharma,Tzu Chi Tseng,Saba Adabi,Simone P. Niclou,Olivier Keunen,Annika Hau,Martin Vallières,David Fortin,Martin Lepage,Bennett A. Landman,Karthik Ramadass,Kaiwen Xu,Silky Chotai,Lola B. Chambless,Akshitkumar M. Mistry,Reid C. Thompson,Yuriy Gusev,Krithika Bhuvaneshwar,Anousheh Sayah,Camelia Bencheqroun,Anas Belouali,Subhashree Madhavan,Thomas C. Booth,Alysha Chelliah,Marc Modat,H. Shuaib,Carmen Dragos,Aly Abayazeed,Kenneth E. Kolodziej,Michael Hill,A. Abbassy,Shady Mohamed Tarek Gamal,Mahmoud Mekhaimar,Mohamed Qayati,Mauricio Reyes,Ji Eun Park,Jihye Yun,Ho Sung Kim,Abhishek Mahajan,Mark Muzi,Sean Benson,Regina G. H. Beets-Tan,Jonas Teuwen,A. Herrera-Trujillo,Maria Trujillo,W. Escobar,Ana Lorena Abello,Jose Bernal,Jhonny C. G'omez,Joseph Choi,Stephen Baek,Yusung Kim,H. Ismael,Bryan G. Allen,John M. Buatti,Aikaterini Kotrotsou,Hongwei Li,Tobias Weiss,Michael Weller,Andrea Bink,B. Pouymayou,Hassan Fathallah Shaykh,Joel H. Saltz,Prateek Prasanna,Sampurna Shrestha,K.M. Mani,David Payne,T. Kurca,Enrique Pelaez,Heydy Franco-Maldonado,Francis R. Loayza,Sebastian Quevedo,Pamela Guevara,Esteban Torche,Cristóbal Mendoza,Franco Vera,Elvis R'ios,E. L'opez,Sergio A. Velastin,Godwin Ogbole,Dotun Oyekunle,O.O Odafe-Oyibotha,Babatunde Ebenezer Osobu,Mustapha Shu’aibu,Adeleye Dorcas,Mayowa Abimbola Soneye,Farouk Dako,Amber L. Simpson,Mohammad Hamghalam,Jacob J. Peoples,Ricky Hu,Anh Tran,D A Cutler,Fabio Y. Moraes,Michael A. Boss,James F. Gimpel,Deepak Kattil Veettil,Kendall Schmidt,Brian Bialecki,S. Marella,Cynthia O. Price,Lisa Cimino,Charles Apgar,Prashant Shah,Bjoern H. Menze,Jill S. Barnholtz-Sloan,Jason Martin,Spyridon Bakas +278 more
TL;DR: This paper presented the largest FL study to date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature.
Journal ArticleDOI
MONAI: An open-source framework for deep learning in healthcare
M. Jorge Cardoso,Wenqi Li,Richard Brown,Nic Ma,Eric Kerfoot,Yiheng Wang,Benjamin Murrey,Andriy Myronenko,Can Zhao,Dong Yang,Vishwesh Nath,Yufan He,Ziyue Xu,Ali Hatamizadeh,Wenjie Zhu,Yun Liu,Mingxin Zheng,Yucheng Tang,Isaac Yang,Michael Zephyr,Behrooz Hashemian,Sachidanand Alle,Mohammad Zalbagi Darestani,C.H. Budd,Marc Modat,Tom Vercauteren,Guotai Wang,Yiwen Li,Yipeng Hu,Yunguan Fu,Benjamin L. Gorman,Hans J. Johnson,Brad W. Genereaux,Barbaros S. Erdal,Vikash Kr Gupta,Andres Diaz-Pinto,Andre Dourson,Lena Maier-Hein,Paul F. Jaeger,Michael Baumgartner,Jayashree Kalpathy–Cramer,Mona Flores,Justin Kirby,Lee Cooper,Holger R. Roth,Daguang Xu,David Bericat,Ralf Floca,S. Kevin Zhou,H. Shuaib,Keyvan Farahani,Klaus H. Maier-Hein,Stephen Aylward,Prerna Dogra,Sebastien Ourselin,Andrew Feng +55 more
TL;DR: MONAI as mentioned in this paper is a framework for deep learning in healthcare, with a particular focus on imaging, and provides purpose-specific transformations and utilities that streamline the development and deployment of medical AI models.
Journal ArticleDOI
Generative Adversarial Networks for Image Augmentation in Agriculture: A Systematic Review
TL;DR: An overview of the evolution of GAN architectures followed by a systematic review of their application to agriculture can be found in this article , involving various vision tasks for plant health, weeds, fruits, aquaculture, animal farming, plant phenotyping as well as postharvest detection of fruit defects.
Journal ArticleDOI
A hybrid machine learning/deep learning COVID-19 severity predictive model from CT images and clinical data
TL;DR: In this article , a hybrid machine learning/deep learning model was developed to classify patients in two outcome categories, non-ICU and ICU (intensive care admission or death), using 558 patients admitted in a northern Italy hospital in February/May of 2020.
References
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