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Hi Felix,
<div><br>
</div>
<div>all the MATLAB functions shipped with each release of Bio-Formats are maintained under</div>
<div><a href="https://github.com/openmicroscopy/bioformats/tree/dev_5_0/components/formats-gpl/matlab">https://github.com/openmicroscopy/bioformats/tree/dev_5_0/components/formats-gpl/matlab</a></div>
<div>for Bio-Formats 5.0.x.</div>
<div><br>
</div>
<div>Cheers</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 12 May 2014, at 13:52, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch">felix.meyenhofer@unifr.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div apple-content-edited="true">Hi Sebastien </div>
<div apple-content-edited="true"><br>
</div>
<div apple-content-edited="true">thanks for pointing out the overlapping method-names. </div>
<div apple-content-edited="true">I will see if I can modify bfGetPlane.m so it is consistent with the example of the OMERO documentation.</div>
<div apple-content-edited="true"><br>
</div>
<div apple-content-edited="true">b.t.w.</div>
<div apple-content-edited="true">is there a public repository for the bioformats-integration for matlab?</div>
<div apple-content-edited="true"><br>
</div>
<div apple-content-edited="true">Best, </div>
<div apple-content-edited="true"><br>
</div>
<div apple-content-edited="true">Felix</div>
<div apple-content-edited="true"><br>
</div>
<br>
<div>
<div>On 12 May 2014, at 12:14 , Sebastien Besson <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>> wrote:</div>
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Hi Felix,<br>
<br>
looking at the Javadoc for Bio-Formats 5.0.1, you raise a confusing point indeed.<br>
<br>
FormatReader.getImageCount() returns the number of image planes for the current series.<br>
This means the output of this method depends on the series index, e.g.
<div>>> reader.setSeries(0);</div>
<div>>> nPlanes1 = reader.getImageCount();<br>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"></blockquote>
>> reader.setSeries(1);<br>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"></blockquote>
>> nPlanes2 = reader.getImageCount();<br>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"></blockquote>
>> nPlanes1 = reader.getMetadataStore().getPlaneCount(0);<br>
>> nPlanes2 = reader.getMetadataStore().getPlaneCount(1);
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</blockquote>
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<br>
See also<br>
<a href="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/loci/formats/FormatReader.html#getImageCount()</a><br>
<a href="http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/ome/xml/meta/MetadataRetrieve.html#getPlaneCount(int)">http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/ome/xml/meta/MetadataRetrieve.html#getPlaneCount(int)</a><br>
<br>
The MetadataRetrieve. getImageCount() returns the total number of Images as defined by the<br>
OME-XML model in the file. This should also be the equivalent of the FormatReader.getSeriesCount()<br>
method,<br>
<blockquote type="cite">
<blockquote type="cite"></blockquote>
</blockquote>
>> nImages = reader.getSeriesCount();<br>
>> nImages = reader.getMetadataStore().getImageCount();<br>
<br>
See also,<br>
<a href="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/ome/xml/meta/MetadataRetrieve.html#getImageCount()</a><br>
<a href="http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/loci/formats/FormatReader.html#getSeriesCount()">http://downloads.openmicroscopy.org/bio-formats/5.0.1/api/loci/formats/FormatReader.html#getSeriesCount()</a><br>
<br>
Hope this answers your question,<br>
Sebastien<br>
<br>
On 9 May 2014, at 15:06, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch">felix.meyenhofer@unifr.ch</a>> wrote:<br>
<br>
<blockquote type="cite">Hi<br>
<br>
<br>
I am a bit confused. From <br>
<a href="http://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html">http://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html</a><br>
we find<br>
reader = bfGetReader('path/to/data/file');<br>
omeMeta = reader.getMetadataStore();<br>
<br>
<br>
But<br>
reader.getImageCount()<br>
and<br>
omeMeta.getImageCount()<br>
do not necessarily return the same number<br>
<br>
I was working on a ndpi-image but tried also a “lighter” lif<br>
<a href="https://dl.dropboxusercontent.com/u/18607042/omero/Pollen_glycerol_20x.lif">https://dl.dropboxusercontent.com/u/18607042/omero/Pollen_glycerol_20x.lif</a><br>
<br>
<blockquote type="cite">From the examples in the documentation I was hoping, that actually allows to determine which plane to load.<br>
</blockquote>
Does somebody hava an idea why this happens? And should it?<br>
<br>
Best, <br>
<br>
Felix<br>
<br>
<br>
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</blockquote>
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<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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