|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.
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
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:
- By specifying the `HDFDatastore`_
widefieldPixelSizeproperty, which is a two-element tuple of the x- and y- pixel sizes.
widefieldPixelSizeis None, the pixel size is extracted from the Micro-Manager metadata in the field specified by
__MM_PixelSize__in B-Store’s config.py.
- If Micro-Manager metadata is not present, look for the pixel size in OME-XML metadata.
- Failing this, the attribute
element_size_umis 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.