Minutes Data Working Group 26 Apr 2020

Agenda

• Review and refine the committee scope
• Task focus: identify the state of the art, and define best practices
• Plan meeting cadence

Attendees

• Invited: Brad Genereaux (Nvidia), Michael Götz (DKFZ), Carole Sudre (KCL), Stephen Aylward (Kitware), Ben Murray (KCL), Wenqi Li (Nvidia), Jorge Cardoso (KCL), Prerna Dogra (NVIDIA)

Notes

• What is the state of art in biomarkers -
  • Preprocessing - trying to make MONAI - “rosetta stone” - make it speak every library for bringing in other libraries. Enabling thoughts, but not much further
  • Pre-processing pipeline built around NIFTI format - data array / offline and spacing orientation.
  • Non-imaging data is classification labels - no principled way to capture this
  • Bounding boxes is being added
  • NLP / communication in EHR is a different problem space - combining imaging and non-imaging data
  • Are their libraries that can be interfaced today that can bring pipelines in?
  • NIFTI is well-prepared for storing imaging data, but not for other data types
• I/O Working Group - getting things off disk and store them in memory
• File structures - XArrays in Python is an emerging standard
  • Preliminary support, not updating meta information
  • Connecting the data with the physical representation
• Metadata for healthcare metadata - FHIR can be used, maybe CDA
  • But what are the use cases? It can be really broad, but too broad = maybe not very useful
• Use cases for people using MONAI
  • Bringing tabular data into MONAI
  • Structured data - ontology tagged, data dictionary and key values
  • Structured data relating to images - coordinates, bounding boxes, imaging elements
  • Unstructured data - free text (NLP), 1D or 2D signals, heart rate, waveforms, movement rates
• How do we make it easy for developers to feed the data to MONAI?
• Design implications for the types of data being brought in
• Use cases with data elements
  • Neuroimaging,
  • COPD
    • Gene expression
  • Ultrasound guided intervention
• How do we connect data together? Imaging and non-imaging data
  • E.g., a table or data dictionary element
  • Define the data types of these elements
  • A data manifest?
• Creating a way to represent “subjects”
• Do we pass along a “bag of content”, or do we need to indicate “prominence” of content?
  • Making it too complex makes it unusable
  • Leveraging DICOM specifications like TID1500 while might be most descriptive might not work well with developers early on
  • Starting with something simple but supporting more complex transactions are ideal
• “Minimal data set” - if the use case demands “just pass along an image and a label”, that should be sufficient - developers shouldn’t have to specify unnecessary content
• Flexible data loader -> standardized internal representations
  • Are there numpy representations that are used in other domains?
• What do we trust exists when things get passed along?
• We should support “if someone passes in a set of JPGs”
• Impact of digital pathology as an example - there’s open challenges in the interoperability space
• A content manifest to define the content
  • Reproducibility
  • Provenance - where the data came from
  • Notion should be shared with the challenge group

Action items

• Brad; Doodle poll
• Brad; manifest
• All; collect use cases -> and types of inputs and outputs (EHR, signals, sensors, genetic data - few markers)
• Carole; put together a template and share with the team