HDF5-Based Data Format for Archiving Complex Neuro-monitoring Data in Traumatic Brain Injury Patients
Objectives: Modern neuro-critical care units generate high volumes of data. These data originate from a multitude of devices in various formats and levels of granularity. We present a new data format intended to store these data in an ordered and homogenous way.
Material and methods: The adopted data format was based on the hierarchical model, HDF5, which is capable of dealing with a mixture of small and very large datasets with equal ease. It is possible to access and manipulate individual data elements directly within a single file, and this is extensible and versatile.
Results: The file structure that was agreed divided the patient data into four different groups: ‘Annotations’ for clinical events and sporadic observations, ‘Numerics’ for all the low-frequency data, ‘Waves’ for all the high-frequency data and ‘Summaries’ for the trend data and calculated parameters. The addition of attributes to every group and dataset makes the file self-described. More than 200 files have been successfully collected and stored using this format.
Conclusion: The new file format was implemented in ICM+ software and validated as part of a collaboration with participating centres across Europe.
KeywordsHDF5 Multimodal monitoring Data storage Data format
This work was supported by a European CoER-TBI).
Conflicts of interest statement
P. Smielewski and M. Czosnyka have partial financial interest in the licensing of ICM+.
- 1.Franklin DF, Ostler DV. Proposed standard IEEE P1073 Medical Information Bus: medical device to host computer interface network overview and architecture. In: Eighth Annual International Phoenix Conference on Computers and Communications 1989 Conference Proceedings. IEEE Comput Soc Press; [cited 2016 Oct 26]. p. 574–8. Available from: http://ieeexplore.ieee.org/document/37448/.
- 2.Maas AIR, Menon DK, Steyerberg EW, Citerio G, Lecky F, Manley GT, et al. Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI): a prospective longitudinal observational study. Neurosurgery [Internet]. 2015 .[cited 2016 Oct 31];76(1):67–80. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25525693.
- 3.HDF5 file format specification version 3.0. Available from: https://support.hdfgroup.org/HDF5/doc/H5.format.html.
- 4.Dougherty MT, Folk MJ, Zadok E, Bernstein HJ, Bernstein FC, Eliceiri KW, et al. Unifying biological image formats with HDF5. Commun AMC. 2009;52(10):42–7.Google Scholar
- 5.Rees N, Billich HR, Koziol Q, Wintersberger E, Götz A, Pourmal E, et al. Developing HDF5 for the Synchrotron Community. 2015;WEPGF063.Google Scholar
- 6.Rübel O, Prabhat M, Denes P, Conant D, Chang E, Bouchard K. BRAINformat: a data standardization framework for neuroscience data. 2015. bioRxiv.Google Scholar
- 7.Eglen SJ, Weeks M, Jessop M, Simonotto J, Jackson T, Sernagor E, et al. A data repository and analysis framework for spontaneous neural activity recordings in developing retina. Gigascience. 2014 [cited 2016 Oct 31];3(1):3. Available from: http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3-3.
- 8.HDF5 Users Guide. [cited 2017 Feb 28]. Available from: https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide.pdf.