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Recommendations for standardized data exchange in photoacoustic imaging Working Group 4

This presentation discusses the mission of Working Group 4 to understand the format of photoacoustic (PA) data available from commercial and custom-built PA imaging instruments, define accompanying metadata, and identify the metadata required for open access and use of data. The current state of PA data formats, metadata parameters, and the standardized data format using HDF5 are discussed. The recommendations include including raw time series data in the standardization, using HDF5 as the standardized file format, and creating a standardized list of metadata parameters.

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Recommendations for standardized data exchange in photoacoustic imaging Working Group 4

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  1. Recommendations for standardized data exchange in photoacoustic imagingWorking Group 4 Presented by Janek Gröhl on behalf of all working group members

  2. Working Group 5 - members Janek Gröhl (Group lead) Hisham Assi Jeff Bamber Richard Bouchard Joanna Brunker Lucia Cavigli Bryan Clingman Germany Canada UK USA UK Italy USA Ben Cox Lina Hacker Drew Heinmiller Stefan Morscher Yoko Okamura Ruiqing Ni Maximillian Waldner UK UK Canada Germany Japan Switzerland Germany of 12

  3. Working Group 4 Mission • Understand the format of PA data available from commercial and custom-built PA imaging instruments • Define a list of accompanying metadata • Identify the metadata that would be required to enable open access and open use of data • Focus near term on commercial imaging instruments of 12

  4. Motivation: Current state of PA data formats • Systems use proprietary file formats • Viewable with vendor specific software • Interfaces to access data: • Python • MATLAB of 12

  5. PAI data format landscape (examples) • iThera Medical, MSOT / RSOM • Proprietary .nod file format • Seno Medical • Proprietary .lom file format • Visualsonics • Proprietary file format • Fraunhofer DiPhAS MITK integration • NRRD file format of 12

  6. Metadata Parameters • Essential parameters to be able to read the raw data • Dimensionality + sizes • Data type • Encoding • Parameters required for reasonable image reconstruction and processing • US transducer design • Illumination geometry • Time domain information • sampling frequency • index of sample which corresponds to zero time • Forquantitativeimageprocessing • the angle and frequency-dependent response of the detectors • Pulse to pulse laser energy of 12

  7. Standardised data format: Requirements • Binary data container with lossless compression • Raw element data needs to be streamable and saveable as a stream • Binary data + metadata in the same file of 12

  8. Good candidate: HDF5 Fulfils all requirements: (1) scalable, open and enables fast access times (2) contains the metadata within the data file → metadata cannot get lost when exchanging files (3) easily accessible without being limited to a specific programming language. → provides interfaces for e.g. C++, Python, MATLAB, and Java. of 12

  9. Recommendation (1) To initially only include raw time series data into the standardization (2) To use HDF5 as the standardized file format (3) To create a standardized list of metadata parameters of 12

  10. Next steps of 12

  11. Next steps of 12

  12. Acknowledgements Chair - Sarah Bohndiek UKCo-Chair - William Vogt USA Working Group Leads • Joanna Brunker UK • James Joseph UK • Lina Hacker UK • Janek Gröhl Germany • William Vogt USA Academic Members Antonio Pifferi Italy Srinath Rajagopal UK Daniel Razansky Germany Avihai Ron Germany Maximillian Waldner Germany Kun Wang China Lihong Wang USA Wenfeng Xia UK Bajram Zeqiri UK Academic Members Thomas Kirchner Germany Jan Klohs Switzerland Lena Maier-Hein Germany Efthymios Maneas UK Julia Mannheim Germany Srirang Manohar Netherlands Lacey McNally USA Luca Menichetti Italy Ruiqing Ni Switzerland Malini Olivo Singapore Marty Pagel USA Geoff Parker UK Anna Pelagotti Belgium Academic Members Paolo Armanetti Italy Hisham Assi Canada Jeff Bamber UK Paul Beard UK Thomas Berer Austria Richard Bouchard USA Kimberly Briggman USA Lucia Cavigli Italy Ben Cox UK Adrien Desjardins UK Jeeseong Hwang USA Eno Hysi Canada Aoife Ivory UK Industrial Members Bryan Clingman USA Drew Heinmiller Canada Jithin Jose Netherlands Steven Miller USA Stefan Morscher Germany Yoko Okamura Japan Lisa Richards USA Mithun Singh Japan www.ipasc.science of 12

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