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Title: F3D Image Processing and Analysis for Many - and Multi-core Platforms

Abstract

F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expedites any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element.more » This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.« less

Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
Wes Bethel, Harinarayan Krishnan, Talita Perciano Costa Leite, Daniela Ushizima
OSTI Identifier:
1231927
Report Number(s):
F3D; 003188MLTPL00
R&D Project: KJ0402000; 2015-031
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Software
Software Revision:
00
Software Package Number:
003188
Software Package Contents:
Open Source Software package available from Lawrence Berkeley National Laboratory at the following URL: http://camera.lbl.gov/software
Software CPU:
MLTPL
Open Source:
Yes
Source Code Available:
No
Related Software:
JOCL and Fiji
Country of Publication:
United States

Citation Formats

. F3D Image Processing and Analysis for Many - and Multi-core Platforms. Computer software. https://www.osti.gov//servlets/purl/1231927. Vers. 00. USDOE. 1 Oct. 2014. Web.
. (2014, October 1). F3D Image Processing and Analysis for Many - and Multi-core Platforms (Version 00) [Computer software]. https://www.osti.gov//servlets/purl/1231927.
. F3D Image Processing and Analysis for Many - and Multi-core Platforms. Computer software. Version 00. October 1, 2014. https://www.osti.gov//servlets/purl/1231927.
@misc{osti_1231927,
title = {F3D Image Processing and Analysis for Many - and Multi-core Platforms, Version 00},
author = {},
abstractNote = {F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expedites any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element. This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.},
url = {https://www.osti.gov//servlets/purl/1231927},
doi = {},
url = {https://www.osti.gov/biblio/1231927}, year = {Wed Oct 01 00:00:00 EDT 2014},
month = {Wed Oct 01 00:00:00 EDT 2014},
note =
}

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