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Hi Alex,
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<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 href="http://qa.openmicroscopy.org.uk/qa/upload/" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a> ?</div>
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<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>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a 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 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>
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<div class="">On 20 Jun 2016, at 21:07, Alexander Al Saroori <<a href="mailto:saroori.alexander@googlemail.com" class="">saroori.alexander@googlemail.com</a>> wrote:</div>
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<p style="margin-bottom: 0cm; line-height: 100%" class="">Hello again,<br class="">
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<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">
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<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>
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<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>
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<br class="">
<div class="moz-cite-prefix">On 20/06/16 19:33, Alexander Al Saroori wrote:<br class="">
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<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>
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</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>
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