OxySoft 4.0 unlocks easy export of NIRS data to .snirf format
Near-Infrared Spectroscopy (NIRS) is a considerably new technology that measures relative concentration changes of oxy- and deoxy-hemoglobin in a local tissue. Due to increasing development also in data analysis and software solutions by different manufacturers, standardized analysis pipelines or data formats for sharing and exchanging data have been lacking. Therefore, researchers active in the field of NIRS worked together on creating a shared file format for NIRS measurements that is compatible with open analysis toolboxes. Read this blog post to learn more about this shared data format and how to easily export your data to .snirf in our software OxySoft.
OxySoft 4.0 meets the .snirf format
We are delighted to announce a significant feature in OxySoft 4.0 and higher: the ability to export measurements directly to the standardized shared near-infrared file (.snirf) format [1]. The shared near-infrared file format (.snirf) is a structured format based on the Hierarchical Data Format (HDF5). It is specifically designed for organizing, storing, and sharing Near-Infrared Spectroscopy (NIRS) data. This format includes essential metadata like stimuli information, transmitter and receiver positions, and measurement date and time.
The .snirf format greatly simplifies the exchange and analysis of (f)NIRS data across diverse hardware and software platforms. It is compatible with various fNIRS analysis tools and software, including Homer3, MNE, FieldTrip, NIRS Brain AnalyzIR, and NIRStorm (for more details, refer to the blog post fNIRS analysis toolbox series – Introduction).
Exporting data to .snirf files in OxySoft is effortless. Watch the following video to learn more on how to export the data to .snirf directly in OxySoft.
Practice with this .snirf data example
To aid users in understanding the .snirf format, we have created two .snirf data examples demonstrating how to load .snirf files into Homer3 [2]. These examples illustrate accessing, exploring, and utilizing metadata (such as stimuli information and transmitter/receiver positions) stored in .snirf files. They also showcase applying a basic processing stream from raw data to an averaged hemodynamic response function (HRF) using Homer3 functions. The repository for these examples can be accessed on GitHub (please see .snirf data example) and can be run directly in MATLAB online. To do so, simply click the "Open in MATLAB Online" button in the repository's readme section.
Conclusion
With the introduction of OxySoft 4.0 and its .snirf export feature, we aim to simplify the sharing of (f)NIRS data. We encourage all users to adopt the .snirf format in their research endeavors, supporting our initiative towards standardization. However, it is important to note that the option to export data to other formats such as .txt, MS Excel, or the proprietary .oxy Artinis format will still be available. For users of OxySoft versions earlier than 4.0, we offer a conversion script called oxysoft2matlab, which also supports .snirf export.
Reach out to us in case of any questions regarding .snirf, or in general at askforinfo@artinis.com.
References
[1] Tucker, S., Dubb, J., Kura, S., von Lühmann, A., Franke, R., Horschig, J. M., Powell, S., Oostenveld, R., Lührs, M., Delaire, É., Aghajan, Z. M., Yun, H., Yücel, M. A., Fang, Q., Huppert, T. J., Frederick, B. B., Pollonini, L., Boas, D., & Luke, R. (2023). Introduction to the shared near infrared spectroscopy format. Neurophotonics, 10(1), 013507.
[2] Huppert, T., Diamond, S., Franceschini, M., Boas, D. (2009). HomER: a review of time-series analysis methods for near-infrared spectroscopy of the brain. Applied optics 48(10).
