学术报告：UFO-KIT Reconstruction Software and User Friendly ImageJ GUI for Synchrotron Imaging Research Community
报告题目: UFO-KIT Reconstruction Software and User Friendly ImageJ GUI for Synchrotron Imaging Research Community
报告人: Dr. Ning Zhu
单位：加拿大光源Canadian Light Source
Ufo-kit (Ultra Fast Online reconstruction by Karlsruhe Institute of Technology) software is an open-source framework for high-speed image acquisition, processing, and CT reconstruction. It facilitates every available hardware device to process tomographic data as fast as possible with on-line reconstruction as the ultimate goal. The BioMedical Imaging & Therapy (BMIT) facility at the Canadian Light Source started to use ufo-kit in order to adapt to the increased demand for high-throughput experiments. Rapid CT reconstruction is important in live animal experiments when it is necessary to quickly confirm, for instance, that the specimen did not move during the scan. Ufo-kit provides a Linux based command-line interface and supports redirection of data between multiple reconstruction steps. The Python wrapper tofu is also available to setup the basic reconstruction routines. In addition, at BMIT, we have developed a user friendly graphical user interface using the popular ImageJ/Fiji environment (ufo-gui). This plugin can be used to generate reconstruction scripts from Linux, Mac OS X, or Windows operating systems. Plugin includes additional helper scripts to automate typical reconstruction tasks such as stitching of multiple vertical tiles with histogram alignment. Importantly, substantial documentation is provided to describe how to batch process typical data acquired at biomedical imaging synchrotron beamlines and prepare volumes for rendering. Ufo-gui has also been designed as a Client-Server model, which can realize automatic task execution, multi-task processing, and multi-client processing. Ufo-kit is an extremely powerful and flexible CT reconstruction software, which permits rapid quality assurance and optimization of reconstruction parameters for beamline scientists. Availability of the ufo-gui together with the descriptive and illustrated manual enables users to complete sophisticated reconstruction tasks too. Experience has indicated that as users become more self-sufficient with data processing it reduces the necessity of lengthy tutoring and supervision by the beamline staff.
Dr. Ning Zhu is a beamline scientist working at the BioMedical Imaging and Therapy (BMIT) beamline at the Canadian Light Source. He specializes in synchrotron based imaging and tissue engineering. Dr. Zhu has a master’s degree in material science and engineering from the Tsinghua University and a Ph.D. degree in biomedical engineering at the University of Saskatchewan. He has joined the BMIT since 2012 and is also an adjunct professor in the Department of Chemical and Biological Engineering at the University of Saskatchewan. Currently, Dr. Zhu is working on BMIT beamline development including design of a new micro-CT system, upgrading imaging detector systems, and development of a new data processing system.