Projects will make image analysis solution more accessible to Python community.
Kitware recently kicked off two National Library of Medicine (NLM) projects to increase synergy between Python and SimpleITK. The efforts will add support for Python in SimpleITK to improve performance and make the open-source, cross-platform system for image analysis easier to build, package, distribute, and install.
“Python is fundamental for open, transparent, and reproducible science,” Jean-Christophe Fillion-Robin, a research and development engineer at Kitware, said. “By adding support for Python, we aim to increase the use of SimpleITK in the scientific Python community.”
The projects aim to better integrate SimpleITK into the scientific Python ecosystem by enhancing SimpleITK packaging and data handling methods, respectively. To enhance packaging, Fillion-Robin is leading a team of experts at Kitware in developing an infrastructure that will permit the distribution of SimpleITK as a Python package. To make this distribution possible, the infrastructure will incorporate a new and reusable Python build tool that will enhance the sustainability of SimpleITK and simplify its installation process.
“Those looking to use SimpleITK for the first time will no longer need advanced knowledge of complex C++ application development,” Fillion-Robin said. “This means that more members of the scientific Python community can take advantage of SimpleITK and its unique capabilities for processing large-scale images in two and three dimensions.”
To refine data handling methods in SimpleITK, an interdisciplinary team from Kitware is working to bridge the system with Python libraries for handling images and arrays. Once completed, the effort will bolster the performance of SimpleITK scripts so that they transfer less data to and from the Python libraries, saving time, decreasing memory usage, and diminishing the potential for performance bottleneck.
“SimpleITK can quickly develop scripts and full-scale applications that leverage the power of the Insight Segmentation and Registration Toolkit (ITK) to ingest image data and perform segmentation and registration,” Patrick Reynolds, a research and development engineer and the leader of the SimpleITK data handling effort at Kitware, said. “Our work will better facilitate the adoption of these scripts and applications into modern analytic workflows.”
SimpleITK is a simplified layer built on ITK. It provides developers with an extensive suite of software tools for use in rapid prototyping, education, and interpreted languages. To learn how to leverage SimpleITK and Kitware’s software development services in fields including medical computing and high-performance visualization, please contact firstname.lastname@example.org.
This material is based upon work funded in whole by two awards from the National Library of Medicine totaling $140,250.