F. Marone1, R. Mokso1, K. Mader1,2, C. Hintermüller1, G. Mikuljan1, A. Isenegger1, M. Stampanoni1,2
1Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
2Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
During its first four years of life, the TOMCAT beamline at the Swiss Light Source has established itself as a state-of-the-art hard X-ray tomographic microscopy endstation for experiments on a large variety of samples, ranging from the field of biology to materials science. It routinely performs absorption as well as phase contrast imaging with an isotropic voxel size ranging from 0.360 up to 14.8 microns. Thanks to the continuous stage rotation during an experiment coupled with the FIFO acquisition mode provided by the used detector, typical scan times are in the order of few minutes, depending on energy and resolution. To take advantage of this acquisition speed and exploit at best the available beamtime, several measures have been developed. From the experiment point of view, in addition to user friendly and automatic tools (e.g. energy change) for the beamlime control, an automatic sample exchanger has been implemented enabling measurement of up to 60 samples, corresponding to several hours of continuous and unattended operation. For the efficient processing of the large amount of data produced, an optimized pipeline has been developed, providing reconstructed tomographic volumes few minutes after the end of a scan. In particular, during acquisition a selection of sinograms is computed on the fly. In this way, immediately after data acquisition, the corresponding reconstructed slices are accessible for quality control through a web interface. The same interface also allows fine tuning of the reconstruction parameters and initiation of the reconstruction of the entire volume on a dedicated computer cluster. The reconstruction speed is increased, without quality degradation, by using an algorithm based on the Fourier Transform method rather than the standard Filter Back-projection routine. Thanks to this integration of all postprocessing algorithms and tools into a pipeline, the necessary user intervention is reduced to a minimum, avoiding errors and dead times and therefore maximizing output.
Ongoing work at TOMCAT is devoted to the development of a dedicated ultrafast (1 Hz) tomographic endstation. The high data rates (> 8Gb/s) provided by this application will required a new concept for data transfer, processing, reconstruction and visualization. Possibilities will be discussed.
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