Converting to Hierarchical Data Format (HDF5)

Converting to Hierarchical Data Format (HDF5)

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

Using the API of PMA.start, one can convert a digital slide to an HDF5 file, where each pyramid level is stored as a three dimensional dataset of RGB values.

You can try this yourself by downloading an example python program that converts a slide to an HDF5 file.

Before you run the program, make sure that the following packages have been installed using the pip command:

  • numpy
  • requests
  • h5py
  • PIL
To run the script issue the following command:
python tohdf5.py "D:/MySlides/slide.mrxs"
Once conversion is complete, you can even visualize the dataset using Panoply:
HDF5

Panoply output