Insight Journal (ISSN 2327-770X) - Integration of the Java Image Science Toolkit with E-Science Platform

Integration of the Java Image Science Toolkit with E-Science Platform

Damon S., Panjwani S., Bao S., Kochunov P., Landman B.

Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/3535

Published in The Insight Journal - 2016 January-December.

Submitted by Stephen Damon on 01-11-2016.

Medical image analyses rely on diverse software packages assembled into a “pipeline”. The Java Image Science Toolkit (JIST) has served as a standalone plugin into the Medical Image Processing Analysis and Visualization (MIPAV). We addressed shortcomings that previously prevented deeper integration of JIST with other E-science platforms. First, we developed an interface for integrating externally compiled packages (similar to the interfaces in NiPy) such that the application can become a “draggable module” in the module tree. This allows for connection of inputs and outputs to other JIST modules while maintaining external processing and monitoring. Second, we develop an integration interface with the Neuroimaging Informatics Tools and Resources Clearinghouse Cloud Environment (NITRC-CE). User can launch and terminate pre-configured nodes to utilize computational resources of the Amazon cloud. Finally, we define a new external data source, which can connect to the eXtensible Neuroimaging Archive Toolkit (XNAT) to query and retrieve remote data using XNAT's REST API. Specifically, we define dataflow for files that can readily be converted into volumes and collections of volumes to interface with any JIST module that expects volumetric image data as an input. Users now have the ability to run their pipelines from a well-defined external data source and no longer are required to already have data on the disk. With these upgrades we have extended JIST’s capabilities outside of complied java source code and enhanced capabilities to seamlessly interface with E-science platforms.

Reviews

There is no review at this time. Be the first to review this publication!

Quick Comments

Comment by Altheqa Stone

https://www.altheqa-eg.com/stone-prices/
https://www.dekorishn-altheqa.com/decoration/
https://www.altheqa-eg.com/stone-types/
https://www.altheqa-stone.com/hashmi-stone-prices/
https://www.decoration-altheqa.com/stone-facades/
https://www.altheqa-stone.com/stone-2020/
https://www.dekorishn-altheqa.com/modern-stone-2/
https://www.dekorishn-altheqa.com/stone-houses/
https://www.altheqa-stone.com/altheqa-stone/
https://www.altheqa-eg.com/black-basalt/
https://www.decoration-altheqa.com/basalt-altheqa/
https://www.altheqa-eg.com/%D8%AA%D8%B1%D9%83%D9%8A%D8%A8-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D9%87%D9%8A%D8%B5%D9%85-%D8%AE%D8%B7%D9%88%D8%A9-%D8%A8%D8%AE%D8%B7%D9%88%D8%A9/
https://www.altheqa-eg.com
https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/
https://www.altheqa-stone.com/stone-decorations/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/export/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/%d8%b3%d8%b9%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%88%d8%b7%d8%b1%d9%8a%d9%82%d9%87-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8%d8%a9/
https://www.altheqa-stone.com/%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%D9%84%D9%85%D8%A7%D8%B0%D8%A7-%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D8%AA%D9%83%D9%84%D9%81-%D8%A7%D9%85%D9%88%D8%A7%D9%84-%D9%83%D8%AB%D9%8A%D8%B1/
https://www.altheqa-stone.com/
https://www.altheqa-stone.com/category/hism-stone/exterior-decorations/
https://www.altheqa-stone.com/stone/
https://www.altheqa-stone.com/stone-altheqa/
https://www.altheqa-stone.com/hism-stone/
https://www.altheqa-stone.com/stone-2/
https://www.altheqa-stone.com/stone-3/
https://www.altheqa-stone.com/stone-decorations/
https://www.altheqa-stone.com/%d9%83%d9%84-%d9%85%d8%a7-%d9%87%d9%88-%d8%ac%d8%af%d9%8a%d8%af-%d9%81%d9%89-%d8%b9%d8%a7%d9%84%d9%85-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%b4%d9%83%d8%a7%d9%84-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%b9%d9%85%d8%a7%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%b3%d9%88%d9%81-%d8%aa%d9%86%d8%a7%d9%84-%d8%a7%d8%b9%d8%ac%d8%a7%d8%a8%d9%83/
https://www.altheqa-stone.com/%d9%85%d9%87%d9%86%d8%af%d8%b3%d9%8a%d9%86-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/export/
https://www.altheqa-stone.com/stone-altheqa/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d9%88%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%85%d9%85%d9%8a%d8%b2%d8%a7%d8%aa-%d9%88%d8%b9%d9%8a%d9%88%d8%a8-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d8%b3%d8%b9%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%88%d8%b7%d8%b1%d9%8a%d9%82%d9%87-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8%d8%a9/
https://www.altheqa-stone.com/%d8%b4%d8%a7%d9%87%d8%af-%d8%a7%d8%ad%d8%af%d8%ab-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%a8%d8%aa%d9%83%d8%a7%d8%b1-%d9%81%d9%89-%d8%a7%d9%84%d8%aa%d8%b5%d9%85%d9%8a%d9%85-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d8%ae%d8%a7%d8%b1%d8%ac%d9%8a%d8%a9/
https://www.altheqa-stone.com/%d8%b4%d8%b1%d9%83%d8%a9-%d8%aa%d8%b5%d8%af%d9%8a%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%85%d9%82%d8%a7%d9%88%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/category/hachmi-stone-facades/
https://www.altheqa-stone.com/category/hism-stone/
https://www.altheqa-stone.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%b3%d9%88%d9%81-%d8%aa%d9%86%d8%a7%d9%84-%d8%a7%d8%b9%d8%ac%d8%a7%d8%a8%d9%83/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d9%88%d9%81%d9%84%d9%84-%d9%81%d8%a7%d8%ae%d8%b1%d8%a9-%d8%a8%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85/
https://www.altheqa-eg.com
https://www.altheqa-eg.com/category/hachemi-stone/
https://www.altheqa-eg.com/%d8%aa%d9%86%d9%81%d9%8a%d8%b0-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/
https://www.altheqa-eg.com/%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ae%d8%a7%d8%b1%d8%ac%d9%8a%d8%a9-%d8%a7%d9%81%d8%b6%d9%84-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d9%88%d9%85%d9%86%d8%a7%d8%b2%d9%84/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a8%d8%a7%d9%84%d8%b5%d9%88%d8%b1-%d9%88%d8%a7%d9%84%d9%81%d8%af%d9%8a%d9%88%d9%87%d8%a7/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%87%d9%88-%d8%a7%d9%84%d8%a7%d9%81%d8%b6%d9%84-%d8%af%d8%a7%d8%a6%d9%85%d8%a7-%d9%84%d9%85%d8%a7%d8%b0%d8%a7%d8%9f/
https://www.altheqa-eg.com/category/stone/
https://www.altheqa-eg.com/%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d8%ae%d8%b7%d9%88%d8%a9-%d8%a8%d8%ae%d8%b7%d9%88%d8%a9/
https://www.altheqa-eg.com/%d8%a7%d8%ad%d8%af%d8%ab-%d9%85%d9%82%d8%a7%d9%84%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ac%d8%b0%d8%a7%d8%a8%d9%87-%d9%85%d9%86-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-eg.com/%d8%a7%d8%b4%d9%83%d8%a7%d9%84-%d9%88%d8%a7%d9%86%d9%88%d8%a7%d8%b9-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d9%84%d9%85%d8%aa%d9%88%d8%a7%d8%ac%d8%af%d9%87/
https://www.altheqa-eg.com/%d8%a7%d8%b4%d9%8a%d8%a7%d8%a1-%d9%8a%d8%ac%d8%a8-%d8%a7%d9%86-%d8%aa%d9%81%d8%b9%d9%84%d9%87%d8%a7-%d9%81%d9%89-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/stone-altheqa/
https://www.altheqa-eg.com/%d8%b4%d8%b1%d9%83%d8%a9-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.pinterest.com/altheqa_stone/%D8%AA%D8%B5%D9%85%D9%8A%D9%85-%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D9%85%D9%86%D8%A7%D8%B2%D9%84-%D9%88%D8%B9%D9%85%D8%A7%D8%B1%D8%A7%D8%AA-%D8%A8%D8%A7%D9%84%D8%AD%D8%AC%D8%B1-%D8%A7%D9%84%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D8%A8%D8%AA%D8%B5%D9%85%D9%8A%D9%85%D8%A7%D8%AA/
https://www.pinterest.com/decoration_altheqa/%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89/
https://www.facebook.com/alth8h/
https://www.pinterest.com/decoration_altheqa/home-design%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D9%87%D9%8A%D8%B5%D9%85/
https://www.dekorishn-altheqa.com/%D8%A7%D8%B3%D8%B9%D8%A7%D8%B1-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89/

https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/

Resources


Download All
Download Paper , View Paper

Statistics more


Global rating:
Review rating:	[review]
Views:	541
Downloads:	2723
Paper Quality:
1 comment

Information more


Paper Id:	963
Categories:	IO, Programming
Keywords:	E-science, pipelines
Tracking Number:	NIH 1R03EB012461, R01EB15611
Revision:
Export citation:
Status:	Open for public review

Share

Linked Publications more


InsightToolkit Kinetic Analysis (itk::ka) Library by Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S.
A MultipleImageIterator for iterating over multiple images simultaneously by Schaerer J.
ITK in Biomedical Research and Commercial Applications by McCormick M., Aylward S., Johnson H., Lowekamp B.
Computing Bone Morphometric Feature Maps from 3-Dimensional Images by Vimort J., McCormick M., Paniagua B.
Automatic Mandible Segmentation on CT Images Using Prior Anatomical Knowledge by Aghdasi N., Li Y., Berens A., Moe K., Hannaford B.
Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach by Lowekamp B., Chen D., Yaniv Z., Yoo T.
OpenCL accelerated GPU binary morphology image filters for ITK by Bardosi Z.
RLEImage: run-length encoded memory compression scheme for an itk::Image by Zukić D., McCormick M., Gerig G., Yushkevich P.
Efficient multithreading for manycore processor: Multidimensional domain decomposition using... by St-Onge E., Scherrer B., Warfield S.K.
A patch-based framework for new ITK functionality: Joint fusion, denoising, and non-local... by Tustison N., Avants B., Wang H., Xie L., Coupe P., Yushkevich P., Manjon J.

View license

Loading license...

Send a message to the author