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Hi Sebastien,<br>
<br>
Thank you very much for your reply! <br>
<br>
Your point was very true, that the problem was the presence of the
log file (which is probably somehow corrupted). After deleting the
logfile it works perfectly. <br>
<br>
Thanks again for your help!<br>
<br>
Best,<br>
Alex<br>
<br>
<div class="moz-cite-prefix">On 21/06/16 13:17, Sebastien Besson
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:A7FD4E27-72CF-4FA6-A105-ED10B9D5659E@dundee.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Alex,
<div class=""><br class="">
</div>
<div class="">thanks for the detailed information, would it be
possible for you to upload a sample file where</div>
<div class="">the stage position is currently missing from
Bio-Formats at</div>
<div class=""><a moz-do-not-send="true"
href="http://qa.openmicroscopy.org.uk/qa/upload/" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a> ?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">The DeltaVision reader uses two different strategies
for reading the stage positions depending</div>
<div class="">on the presence of a log file and the number of
series [1] [2]. It might be there is a case where</div>
<div class="">the information needs to be parsed properly.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L766"
class="">https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L766</a></div>
<div class="">[2] <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L1191"
class="">https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L1191</a></div>
<div class=""><br class="">
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 20 Jun 2016, at 21:07, Alexander Al
Saroori <<a moz-do-not-send="true"
href="mailto:saroori.alexander@googlemail.com"
class="">saroori.alexander@googlemail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Hello again,<br class="">
</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Sorry for emailing you again but I've just
got the hint, that I should be more specific, since
there are different DV files. That's why I tried all
different DV data stacks I got so far from a OMX-V3
microsocope. <br class="">
</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Retrieving the stage position from the meta
data in Matlab works very good for (processed) data
stacks using the provided software from Deltavision
(Softworx). So I can get the information from
reconstructed 3D SIM-stacks, image stacks acquired
in STORM mode(which are technically just single
widefield images in a time series) and 3D
deconvoluted stacks.<br class="">
</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Unfortunately it does not work for
unprocessed SIM stacks, conventional 3D-stacks and
which is why I am writing for data stacks with
several time points and just one z-position.
(experimental setup: 5000 images (every 10ms one
image)). I know that the information of the stage
position is stored in the data stacks since I can
get the information using Softworx.<br class="">
</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Working minimal code for 3D-Stack (several
z-slices)</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">r= bfGetReader(fpath);<br class="">
m = r.getMetadataStore();<br class="">
m.getPlanePositionZ(0, 0)</p>
<div style="margin-bottom: 0cm; line-height: 100%;"
class=""><br class="webkit-block-placeholder">
</div>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">ans = ome.units.quantity.Length:
value[3612.2], unit[reference frame] stored as
java.lang.Float</p>
<div style="margin-bottom: 0cm; line-height: 100%;"
class=""><br class="webkit-block-placeholder">
</div>
<p style="margin-bottom: 0cm; line-height: 100%"
class=""><br class="">
For the data stack with several time points, I just
got</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">ans = []</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Do I miss something, or is there any other
commando I could use to get this information from my
data stack?</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Thank you very much!</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Cheers,</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Alex</p>
<br class="">
<br class="">
<div class="moz-cite-prefix">On 20/06/16 19:33,
Alexander Al Saroori wrote:<br class="">
</div>
<blockquote cite="mid:576836F4.5090303@googlemail.com"
type="cite" class="">
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Hi together,</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">I have some problems to get the camera
position stored in the metadata of my deltavision
(DV) files, using Bio-Formats in Matlab. It works
very good for single image stacks (with several
z-slices) but not for data stacks with several
timepoints and just one z-position. (experimental
setup: 5000 images (every 10ms one image)). I know
that the information of the camera position is
stored in the time series since I can get the
information using Softworx (provided Deltavision
software).</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Working minimal code for 3D-Stack
(several z-slices)</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">r= bfGetReader(fpath);<br class="">
m = r.getMetadataStore();<br class="">
m.getPlanePositionZ(0, 0)</p>
<div style="margin-bottom: 0cm; line-height: 100%;"
class=""><br class="webkit-block-placeholder">
</div>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">ans = ome.units.quantity.Length:
value[3612.2], unit[reference frame] stored as
java.lang.Float</p>
<div style="margin-bottom: 0cm; line-height: 100%;"
class=""><br class="webkit-block-placeholder">
</div>
<p style="margin-bottom: 0cm; line-height: 100%"
class=""><br class="">
For the data stack with several timepoints, I just
got</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">ans = []</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Do I miss something, or is there any
other commando I could use to get this information
from my data stack?</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Thank you very much!</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Cheers,</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class="">Alex</p>
<p style="margin-bottom: 0cm; line-height: 100%"
class=""><br class="">
</p>
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