[ome-users] bfmatlab metadata access

[Sebastien Besson]

Hi Felix,

all the MATLAB functions shipped with each release of Bio-Formats are maintained under
https://github.com/openmicroscopy/bioformats/tree/dev_5_0/components/formats-gpl/matlab
for Bio-Formats 5.0.x.

Cheers
Sebastien

On 12 May 2014, at 13:52, MEYENHOFER Felix <felix.meyenhofer at unifr.ch<mailto:felix.meyenhofer at unifr.ch>> wrote:

Hi Sebastien

thanks for pointing out the overlapping method-names.
I will see if I can modify bfGetPlane.m so it is consistent with the example of the OMERO documentation.

b.t.w.
is there a public repository for the bioformats-integration for matlab?

Best,

Felix


On 12 May 2014, at 12:14 , Sebastien Besson <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:

Hi Felix,

looking at the Javadoc for Bio-Formats 5.0.1, you raise a confusing point indeed.

FormatReader.getImageCount() returns the number of image planes for the current series.
This means the output of this method depends on the series index, e.g.
>> reader.setSeries(0);
>> nPlanes1 = reader.getImageCount();
>> reader.setSeries(1);
>> nPlanes2 = reader.getImageCount();
>> nPlanes1 = reader.getMetadataStore().getPlaneCount(0);
>> nPlanes2 = reader.getMetadataStore().getPlaneCount(1);

See also
http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/loci/formats/FormatReader.html#getImageCount()
http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/ome/xml/meta/MetadataRetrieve.html#getPlaneCount(int)

The MetadataRetrieve. getImageCount() returns the total number of Images as defined by the
OME-XML model in the file. This should also be the equivalent of the FormatReader.getSeriesCount()
method,
>> nImages = reader.getSeriesCount();
>> nImages = reader.getMetadataStore().getImageCount();

See also,
http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/ome/xml/meta/MetadataRetrieve.html#getImageCount()
http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/loci/formats/FormatReader.html#getSeriesCount()

Hope this answers your question,
Sebastien

On 9 May 2014, at 15:06, MEYENHOFER Felix <felix.meyenhofer at unifr.ch<mailto:felix.meyenhofer at unifr.ch>> wrote:

Hi


I am a bit confused. From
http://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html
we find
reader = bfGetReader('path/to/data/file');
omeMeta = reader.getMetadataStore();


But
reader.getImageCount()
and
omeMeta.getImageCount()
do not necessarily return the same number

I was working on a ndpi-image but tried also a “lighter” lif
https://dl.dropboxusercontent.com/u/18607042/omero/Pollen_glycerol_20x.lif

>From the examples in the documentation I was hoping, that actually allows to determine which plane to load.
Does somebody hava an idea why this happens? And should it?

Best,

Felix


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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096


Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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