HDF and OME

Paris 2015

OME team

Outline

  • What is HDF5?
  • Status update
  • Discussion

What is HDF5?

  • A data model.
  • A library.
  • A file format for storing and managing data.

CellH5

  • HDF5 data format for cell-based assays in HCS
  • stored image medata with object measurements
  • stored inter-object relations
  • CellH5Browser: image browser based on CellH5
  • Open source LGPL license
  • Bio-Formats support: CellH5Reader
  • To come: CellH5Writer (thanks C. Sommer)

Bitplane Imaris 5.5

BigDataViewer

  • Re-slicing browser for terabyte-sized multi-view image sequences.
  • Comes with custom file format based on XML (for metadata) and HDF5 (for raw data).
  • Open source GPL license

Discusssion