The cancer imaging phenomics toolkit (CaPTk): Technical overview

Sarthak Pati, Ashish Singh, Saima Rathore, Aimilia Gastounioti, Mark Bergman, Phuc Ngo, Sung Min Ha, Dimitrios Bounias, James Minock, Grayson Murphy, Hongming Li, Amit Bhattarai, Adam Wolf, Patmaa Sridaran, Ratheesh Kalarot, Hamed Akbari, Aristeidis Sotiras, Siddhesh P. Thakur, Ragini Verma, Russell T. ShinoharaPaul Yushkevich, Yong Fan, Despina Kontos, Christos Davatzikos, Spyridon Bakas

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

33 Scopus citations


The purpose of this manuscript is to provide an overview of the technical specifications and architecture of the Cancer imaging Phenomics Toolkit (CaPTk, a cross-platform, open-source, easy-to-use, and extensible software platform for analyzing 2D and 3D images, currently focusing on radiographic scans of brain, breast, and lung cancer. The primary aim of this platform is to enable swift and efficient translation of cutting-edge academic research into clinically useful tools relating to clinical quantification, analysis, predictive modeling, decision-making, and reporting workflow. CaPTk builds upon established open-source software toolkits, such as the Insight Toolkit (ITK) and OpenCV, to bring together advanced computational functionality. This functionality describes specialized, as well as general-purpose, image analysis algorithms developed during active multi-disciplinary collaborative research studies to address real clinical requirements. The target audience of CaPTk consists of both computational scientists and clinical experts. For the former it provides i) an efficient image viewer offering the ability of integrating new algorithms, and ii) a library of readily-available clinically-relevant algorithms, allowing batch-processing of multiple subjects. For the latter it facilitates the use of complex algorithms for clinically-relevant studies through a user-friendly interface, eliminating the prerequisite of a substantial computational background. CaPTk’s long-term goal is to provide widely-used technology to make use of advanced quantitative imaging analytics in cancer prediction, diagnosis and prognosis, leading toward a better understanding of the biological mechanisms of cancer development.

Original languageEnglish
Title of host publicationBrainlesion
Subtitle of host publicationGlioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 5th International Workshop, BrainLes 2019, Held in Conjunction with MICCAI 2019, Revised Selected Papers
EditorsAlessandro Crimi, Spyridon Bakas
Number of pages15
ISBN (Print)9783030466428
StatePublished - 2020
Event5th International MICCAI Brainlesion Workshop, BrainLes 2019, held in conjunction with the Medical Image Computing for Computer Assisted Intervention, MICCAI 2019 - Shenzhen, China
Duration: Oct 17 2019Oct 17 2019

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11993 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference5th International MICCAI Brainlesion Workshop, BrainLes 2019, held in conjunction with the Medical Image Computing for Computer Assisted Intervention, MICCAI 2019


  • Brain tumor
  • Breast cancer
  • CaPTk
  • Cancer
  • Deep learning
  • Glioblastoma
  • Glioma
  • ITCR
  • Imaging
  • Lung cancer
  • Phenomics
  • Radiogenomics
  • Radiomics
  • Radiophenotype
  • Segmentation
  • Toolkit


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