Grace Gyamfuah Yamoah1, Liji Cao2, Chao Wu Wu3,4, Freek J Beekman3,4, Bert Vandeghinste5, Julia G Mannheim6, Stefanie Rosenhain1,7, Kevin Leonardic1,7, Fabian Kiessling1,8, Felix Gremse9,10. 1. Institute for Experimental Molecular Imaging, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Clinic, Forckenbeckstraße 55, 52074, Aachen, Germany. 2. Inviscan SAS, Strasbourg, France. 3. MILabs B.V. Utrecht, Utrecht, The Netherlands. 4. Radiation Science & Technology, Delft University of Technology, Delft, the Netherlands. 5. Molecubes NV, Ghent, Belgium. 6. Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, Eberhard Karls University Tuebingen, Tuebingen, Germany. 7. Gremse-IT GmbH, Aachen, Germany. 8. Comprehensive Diagnostic Center Aachen, RWTH Aachen University Clinic, Aachen, Germany. 9. Institute for Experimental Molecular Imaging, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Clinic, Forckenbeckstraße 55, 52074, Aachen, Germany. fgremse@ukaachen.de. 10. Gremse-IT GmbH, Aachen, Germany. fgremse@ukaachen.de.
Abstract
PURPOSE: In biomedical research, imaging modalities help discover pathological mechanisms to develop and evaluate novel diagnostic and theranostic approaches. However, while standards for data storage in the clinical medical imaging field exist, data curation standards for biomedical research are yet to be established. This work aimed at developing a free secure file format for multimodal imaging studies, supporting common in vivo imaging modalities up to five dimensions as a step towards establishing data curation standards for biomedical research. PROCEDURES: Images are compressed using lossless compression algorithm. Cryptographic hashes are computed on the compressed image slices. The hashes and compressions are computed in parallel, speeding up computations depending on the number of available cores. Then, the hashed images with digitally signed timestamps are cryptographically written to file. Fields in the structure, compressed slices, hashes, and timestamps are serialized for writing and reading from files. The C++ implementation is tested on multimodal data from six imaging sites, well-documented, and integrated into a preclinical image analysis software. RESULTS: The format has been tested with several imaging modalities including fluorescence molecular tomography/x-ray computed tomography (CT), positron emission tomography (PET)/CT, single-photon emission computed tomography/CT, and PET/magnetic resonance imaging. To assess performance, we measured the compression rate, ratio, and time spent in compression. Additionally, the time and rate of writing and reading on a network drive were measured. Our findings demonstrate that we achieve close to 50 % reduction in storage space for μCT data. The parallelization speeds up the hash computations by a factor of 4. We achieve a compression rate of 137 MB/s for file of size 354 MB. CONCLUSIONS: The development of this file format is a step to abstract and curate common processes involved in preclinical and clinical multimodal imaging studies in a standardized way. This work also defines better interface between multimodal imaging modalities and analysis software.
PURPOSE: In biomedical research, imaging modalities help discover pathological mechanisms to develop and evaluate novel diagnostic and theranostic approaches. However, while standards for data storage in the clinical medical imaging field exist, data curation standards for biomedical research are yet to be established. This work aimed at developing a free secure file format for multimodal imaging studies, supporting common in vivo imaging modalities up to five dimensions as a step towards establishing data curation standards for biomedical research. PROCEDURES: Images are compressed using lossless compression algorithm. Cryptographic hashes are computed on the compressed image slices. The hashes and compressions are computed in parallel, speeding up computations depending on the number of available cores. Then, the hashed images with digitally signed timestamps are cryptographically written to file. Fields in the structure, compressed slices, hashes, and timestamps are serialized for writing and reading from files. The C++ implementation is tested on multimodal data from six imaging sites, well-documented, and integrated into a preclinical image analysis software. RESULTS: The format has been tested with several imaging modalities including fluorescence molecular tomography/x-ray computed tomography (CT), positron emission tomography (PET)/CT, single-photon emission computed tomography/CT, and PET/magnetic resonance imaging. To assess performance, we measured the compression rate, ratio, and time spent in compression. Additionally, the time and rate of writing and reading on a network drive were measured. Our findings demonstrate that we achieve close to 50 % reduction in storage space for μCT data. The parallelization speeds up the hash computations by a factor of 4. We achieve a compression rate of 137 MB/s for file of size 354 MB. CONCLUSIONS: The development of this file format is a step to abstract and curate common processes involved in preclinical and clinical multimodal imaging studies in a standardized way. This work also defines better interface between multimodal imaging modalities and analysis software.
Authors: Felix Gremse; Christoph Grouls; Moritz Palmowski; Twan Lammers; Anke de Vries; Holger Grüll; Marco Das; Georg Mühlenbruch; Shamima Akhtar; Andreas Schober; Fabian Kiessling Journal: Radiology Date: 2011-07-25 Impact factor: 11.105
Authors: Sijumon Kunjachan; Felix Gremse; Benjamin Theek; Patrick Koczera; Robert Pola; Michal Pechar; Tomas Etrych; Karel Ulbrich; Gert Storm; Fabian Kiessling; Twan Lammers Journal: ACS Nano Date: 2012-10-24 Impact factor: 15.881
Authors: Thomas Pöschinger; Anja Renner; Fabian Eisa; Michael Dobosz; Steffen Strobel; Thomas G Weber; Robert Brauweiler; Willi A Kalender; Werner Scheuer Journal: Invest Radiol Date: 2014-07 Impact factor: 6.016
Authors: Felix Gremse; Marius Stärk; Josef Ehling; Jan Robert Menzel; Twan Lammers; Fabian Kiessling Journal: Theranostics Date: 2016-01-01 Impact factor: 11.556