<div dir="ltr">Hi Sebastien,<div><br></div><div>Yes, that worked.</div><div><br></div><div>Thanks a lot to you and to Melissa for the great support.</div><div><br></div><div>--</div><div>Fethallah</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 23, 2015 at 10:34 AM, Sebastien Besson (Staff) <span dir="ltr"><<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Fethallah,
<div><br>
</div>
<div>according to the ReaderWrapper.<a href="http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)" target="_blank">setFlattenedResolutions</a> Javadoc [1],</div>
<div>you may want to try the following on MATLAB:</div>
<div><br>
</div>
<div>>> reader.setFlattenedResolutions(false);</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>[1] <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)" target="_blank">http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)</a><div><div class="h5"><br>
<div>
<blockquote type="cite">
<div>On 23 Jul 2015, at 09:19, Fethallah Benmansour <<a href="mailto:fethallah.benmansour@gmail.com" target="_blank">fethallah.benmansour@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Dear Mellissa,
<div><br>
</div>
<div>Thanks for your prompts answer.</div>
<div><br>
</div>
<div>Unfortunately, we're having an error when executing </div>
<div><span style="font-size:12.8000001907349px">reader.</span><span style="font-size:12.8000001907349px">setFlattenedResolutions('</span><span style="font-size:12.8000001907349px">false');</span><br>
</div>
<div><span style="font-size:12.8000001907349px">>> No method 'setFlattenedResolutions' with matching signature found for class</span></div>
<div><span style="font-size:12.8000001907349px">'loci.formats.ChannelSeparator'.</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">We double checked that we are using the latest version of bfmatlab (and bioformats_package.jar).</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">Could you please help ?</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">Best,</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">--</span></div>
<div><span style="font-size:12.8000001907349px">Fethallah</span></div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jul 22, 2015 at 9:12 PM, Melissa Linkert <span dir="ltr">
<<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Fethallah,<br>
<span><br>
> From Matlab, we are using the the bioformat toolbox to read vsi files<br>
> (cellSens VSI from Olympus).<br>
><br>
> The vsi file is pointing to a few frame_t.ets files located in<br>
> sub-directories as follows:<br>
> --- stack1 : code bar (not interesting for us)<br>
> --- stack10000 : low resolution whole slide image (not interesting for<br>
> us)<br>
> --- stack10002 : high resolution image of a selected box<br>
> --- stack10005 : high res image of an other selected box<br>
><br>
> Our problem is that even if we specify to the bfGetReader function to read<br>
> the file under stack10005/frame_t.ets, it is reading stack10002/frame_t.ets<br>
> instead.<br>
<br>
</span>The .ets files are always grouped together with the corresponding .vsi<br>
file, so this is expected. Choosing any one of the files from the<br>
dataset will initialize the whole dataset when bfGetReader is called.<br>
<span><br>
> Is there a way to force it to read a specific stack from the slide ?<br>
> From the java code, it seems that when an *.ets file is passed then it<br>
> point back to the associated vsi file...<br>
<br>
</span>The easiest way to do that is something like:<br>
<br>
%%%<br>
reader = bfGetReader(); % do not specify the file name just yet<br>
reader.setFlattenedResolutions('false');<br>
reader.setId('name_of_file.vsi'); % an .ets file name can also be used here<br>
<br>
% numberOfStacks should be 5 in the above example<br>
% one for each .ets file, and one for the .vsi file<br>
numberOfStacks = reader.getSeriesCount();<br>
<br>
% this should specify 'stack10005'; the .ets files are<br>
% in the same order as their respective directory names, and<br>
% the .vsi file is last<br>
stackIndex = numberOfStacks - 1;<br>
reader.setSeries(stackIndex);<br>
<br>
% now the reader is set to retrieve the correct images<br>
% when using bfGetPlane (you may need to modify this call<br>
% to retrieve a tile instead of the whole image)<br>
image = bfGetPlane(reader, 0);<br>
%%%<br>
<br>
If that doesn't work, please let us know.<br>
<br>
Regards,<br>
-Melissa<br>
<div>
<div><br>
On Wed, Jul 22, 2015 at 05:28:43PM +0200, Fethallah Benmansour wrote:<br>
> Dear Support,<br>
><br>
> From Matlab, we are using the the bioformat toolbox to read vsi files<br>
> (cellSens VSI from Olympus).<br>
><br>
> The vsi file is pointing to a few frame_t.ets files located in<br>
> sub-directories as follows:<br>
> --- stack1 : code bar (not interesting for us)<br>
> --- stack10000 : low resolution whole slide image (not interesting for<br>
> us)<br>
> --- stack10002 : high resolution image of a selected box<br>
> --- stack10005 : high res image of an other selected box<br>
><br>
> Our problem is that even if we specify to the bfGetReader function to read<br>
> the file under stack10005/frame_t.ets, it is reading stack10002/frame_t.ets<br>
> instead.<br>
><br>
> Is there a way to force it to read a specific stack from the slide ?<br>
> From the java code, it seems that when an *.ets file is passed then it<br>
> point back to the associated vsi file...<br>
><br>
> Thank you into advance,<br>
><br>
> Kind regards,<br>
><br>
> --<br>
> Fethallah<br>
<br>
</div>
</div>
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