Data Curation for Preclinical and Clinical Multimodal Imaging Studies
Data Curation for Preclinical and Clinical Multimodal Imaging Studies
复制标题
临床前和临床多模态成像研究的数据管理
DOI：
10.1007/s11307-019-01339-0
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发表时间：
2019
影响因子：
3.1
通讯作者：
F. Gremse
中科院分区：
文献类型：
--
作者：
G. G. Yamoah;Liji Cao;Chao Wu;F. Beekman;B. Vandeghinste;J. Mannheim;S. Rosenhain;Kevin Leonardic;F. Kiessling;F. Gremse
目的在生物医学研究中，成像方式有助于发现病理机制，以开发和评估新的诊断和治疗方法。然而，尽管临床医学影像领域的数据存储标准已经存在，但生物医学研究的数据管理标准尚未建立。这项工作旨在为多模式成像研究开发一种免费的安全文件格式，支持高达5维的常见活体成像模式，作为建立生物医学研究数据管理标准的一步。过程使用无损压缩算法压缩图像。在压缩的图像切片上计算加密散列。散列和压缩是并行计算的，根据可用核心的数量加快了计算速度。然后，将具有数字签名时间戳的散列图像以加密方式写入文件。结构中的字段、压缩切片、散列和时间戳被序列化，以便从文件中写入和读取。C++实现在6个成像站点的多模式数据上进行了测试，并被集成到临床前图像分析软件中。结果该格式已经在几种成像方式下进行了测试，包括荧光分子断层扫描/X射线计算机断层扫描(CT)、正电子发射断层扫描(PET)/CT、单光子发射计算机断层扫描/CT和PET/磁共振成像。为了评估性能，我们测量了压缩率、比率和压缩时间。此外，还测量了在网络驱动器上写入和读取的时间和速率。我们的研究结果表明，我们将μCT数据的存储空间减少了近50%。对于大小为354MB的文件，我们的压缩比达到137万亿MB/S。结论该文件格式的开发是以标准化的方式抽象和整理临床前和临床多模式成像研究中涉及的常见过程的一步。这项工作还定义了多模式成像模式和分析软件之间更好的接口。
PurposeIn 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.ProceduresImages 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.ResultsThe 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.ConclusionsThe 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.
影响因子：
17.1
作者：
Kunjachan S;Gremse F;Theek B;Koczera P;Pola R;Pechar M;Etrych T;Ulbrich K;Storm G;Kiessling F;Lammers T
通讯作者：
Lammers T