Using B-Store with Other Software

Author:Kyle M. Douglass
organization:École Polytechnique Fédérale de Lausanne (EPFL)
revision:$Revision: 1 $
abstract:B-Store uses the HDF file format, which means it may be used with other software programs for bio-image analysis.

B-Store databases use the HDF file format for data storage. This means that any software package that can read from HDF files can also read B-Store databases.

ImageJ and Fiji

Widefield images found inside a B-Store database may be opened in ImageJ and Fiji using the HDF5 Plugin for ImageJ and Fiji. When using the GUI loader, use the option individual hyperstacks (custom layout) with yz as the data set layout argument.

This functionality requires that the image data in the HDF file possess an attribute called element_size_um that contains three floating point numbers corresponding to the size of a pixel in z, y, and x-directions. There are three ways that this attribute may be created when the database is built:

  1. By specifying the `HDFDatastore`_ widefieldPixelSize property, which is a two-element tuple of the x- and y- pixel sizes.
  2. If widefieldPixelSize is None, the pixel size is extracted from the Micro-Manager metadata in the field specified by __MM_PixelSize__ in B-Store’s
  3. If Micro-Manager metadata is not present, look for the pixel size in OME-XML metadata.
  4. Failing this, the attribute element_size_um is not set.

If the images were not generated by Micro-Manager or a program that writes OME-XML metadata, simply specify the pixel size in the widefieldPixelSize attribute described above.