Open Microscopy Environment

Hi

I have downloaded the latest Bioformats Matlab toolbox and have followed the tutorial here:

http://www.openmicroscopy.org/site/supp ... b-dev.html

bfopen uses getSeriesMetadata to retrieve a hashtable for the metadata. Unfortunately this method produces an empty hashtable. I had to modify this to use the getMetadata method instead.

Cheers,

Dan.

Hi Dan,

thanks for the bug report. You are right, the current implementation of bfopen.m does not include the global metadata but only the series-specific metadata. This change was originally implemented to prevent all metadata to be read for all series in large multi-series files (see the corresponding thread at http://lists.openmicroscopy.org.uk/pipe ... 03825.html).

Depending on the format you are reading, the metadata may either be stored in the global or the series metadata. Using getMetadata as you suggest will indeed give you access to all the metadata.

Note however that this method returns the global metadata and the metadata for all the series in the file. We are currently working on a bug fix to correctly store the original metadata both global and series-specific in the output of bfopen.m (see https://github.com/openmicroscopy/bioformats/pull/825).

Cheers,
Sebastien