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Hi Fethallah,
<div class=""><br class="">
</div>
<div class="">according to the ReaderWrapper.<a href="http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)" class="">setFlattenedResolutions</a> Javadoc [1],</div>
<div class="">you may want to try the following on MATLAB:</div>
<div class=""><br class="">
</div>
<div class="">>> reader.setFlattenedResolutions(false);</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)" class="">http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)</a><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 23 Jul 2015, at 09:19, Fethallah Benmansour <<a href="mailto:fethallah.benmansour@gmail.com" class="">fethallah.benmansour@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Dear Mellissa,
<div class=""><br class="">
</div>
<div class="">Thanks for your prompts answer.</div>
<div class=""><br class="">
</div>
<div class="">Unfortunately, we're having an error when executing </div>
<div class=""><span style="font-size:12.8000001907349px" class="">reader.</span><span style="font-size:12.8000001907349px" class="">setFlattenedResolutions('</span><span style="font-size:12.8000001907349px" class="">false');</span><br class="">
</div>
<div class=""><span style="font-size:12.8000001907349px" class="">>> No method 'setFlattenedResolutions' with matching signature found for class</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">'loci.formats.ChannelSeparator'.</span></div>
<div class=""><span style="font-size:12.8000001907349px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">We double checked that we are using the latest version of bfmatlab (and bioformats_package.jar).</span></div>
<div class=""><span style="font-size:12.8000001907349px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">Could you please help ?</span></div>
<div class=""><span style="font-size:12.8000001907349px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">Best,</span></div>
<div class=""><span style="font-size:12.8000001907349px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">--</span></div>
<div class=""><span style="font-size:12.8000001907349px" class="">Fethallah</span></div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Wed, Jul 22, 2015 at 9:12 PM, Melissa Linkert <span dir="ltr" class="">
<<a href="mailto:melissa@glencoesoftware.com" target="_blank" class="">melissa@glencoesoftware.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Fethallah,<br class="">
<span class=""><br class="">
> From Matlab, we are using the the bioformat toolbox to read vsi files<br class="">
> (cellSens VSI from Olympus).<br class="">
><br class="">
> The vsi file is pointing to a few frame_t.ets files located in<br class="">
> sub-directories as follows:<br class="">
> --- stack1 : code bar (not interesting for us)<br class="">
> --- stack10000 : low resolution whole slide image (not interesting for<br class="">
> us)<br class="">
> --- stack10002 : high resolution image of a selected box<br class="">
> --- stack10005 : high res image of an other selected box<br class="">
><br class="">
> Our problem is that even if we specify to the bfGetReader function to read<br class="">
> the file under stack10005/frame_t.ets, it is reading stack10002/frame_t.ets<br class="">
> instead.<br class="">
<br class="">
</span>The .ets files are always grouped together with the corresponding .vsi<br class="">
file, so this is expected. Choosing any one of the files from the<br class="">
dataset will initialize the whole dataset when bfGetReader is called.<br class="">
<span class=""><br class="">
> Is there a way to force it to read a specific stack from the slide ?<br class="">
> From the java code, it seems that when an *.ets file is passed then it<br class="">
> point back to the associated vsi file...<br class="">
<br class="">
</span>The easiest way to do that is something like:<br class="">
<br class="">
%%%<br class="">
reader = bfGetReader(); % do not specify the file name just yet<br class="">
reader.setFlattenedResolutions('false');<br class="">
reader.setId('name_of_file.vsi'); % an .ets file name can also be used here<br class="">
<br class="">
% numberOfStacks should be 5 in the above example<br class="">
% one for each .ets file, and one for the .vsi file<br class="">
numberOfStacks = reader.getSeriesCount();<br class="">
<br class="">
% this should specify 'stack10005'; the .ets files are<br class="">
% in the same order as their respective directory names, and<br class="">
% the .vsi file is last<br class="">
stackIndex = numberOfStacks - 1;<br class="">
reader.setSeries(stackIndex);<br class="">
<br class="">
% now the reader is set to retrieve the correct images<br class="">
% when using bfGetPlane (you may need to modify this call<br class="">
% to retrieve a tile instead of the whole image)<br class="">
image = bfGetPlane(reader, 0);<br class="">
%%%<br class="">
<br class="">
If that doesn't work, please let us know.<br class="">
<br class="">
Regards,<br class="">
-Melissa<br class="">
<div class="">
<div class="h5"><br class="">
On Wed, Jul 22, 2015 at 05:28:43PM +0200, Fethallah Benmansour wrote:<br class="">
> Dear Support,<br class="">
><br class="">
> From Matlab, we are using the the bioformat toolbox to read vsi files<br class="">
> (cellSens VSI from Olympus).<br class="">
><br class="">
> The vsi file is pointing to a few frame_t.ets files located in<br class="">
> sub-directories as follows:<br class="">
> --- stack1 : code bar (not interesting for us)<br class="">
> --- stack10000 : low resolution whole slide image (not interesting for<br class="">
> us)<br class="">
> --- stack10002 : high resolution image of a selected box<br class="">
> --- stack10005 : high res image of an other selected box<br class="">
><br class="">
> Our problem is that even if we specify to the bfGetReader function to read<br class="">
> the file under stack10005/frame_t.ets, it is reading stack10002/frame_t.ets<br class="">
> instead.<br class="">
><br class="">
> Is there a way to force it to read a specific stack from the slide ?<br class="">
> From the java code, it seems that when an *.ets file is passed then it<br class="">
> point back to the associated vsi file...<br class="">
><br class="">
> Thank you into advance,<br class="">
><br class="">
> Kind regards,<br class="">
><br class="">
> --<br class="">
> Fethallah<br class="">
<br class="">
</div>
</div>
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</blockquote>
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</blockquote>
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