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<p>Hi OME team,</p>
<p>I ran into an issue with a Zeiss *.czi produced by the Axioscan
Slidescanner. This dataset (<a moz-do-not-send="true"
href="https://filesender.switch.ch/filesender/?vid=26acedaa-f108-7348-ca3a-00006ae0f68d">download,
530 MB</a>) contains:
<br>
1 scene,
23 unstitched tiles 2040 x 2040
, 2 channels
, 3 z
, 1
overview and 1 label image <br>
</p>
<p>I wanted to open this file using the latest BF 5.6 SNAPSHOT with
stitching checked to have the tiles stitched by their stage
coordinates.</p>
<p>What happened however is that it opened all images individually
instead of stitched. Is it possible that there was a problem
recognising the tile positions?</p>
<p>Here is what I tried:<br>
</p>
<p>run("Bio-Formats Importer",
"open=V:\\Axioscan_stitching\\20170814-20xFL-1sc-2C-3z_nostitch_nopyramid\\20170814-20xFL-1sc-2C-3z_nostitch_nopyramid.czi
autoscale color_mode=Default display_metadata display_ome-xml
rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT
stitch_tiles series_1 series_2 series_3 series_4 series_5 series_6
series_7 series_8 series_9 series_10 series_11 series_12 series_13
series_14 series_15 series_16 series_17 series_18 series_19
series_20 series_21 series_22 series_23");
<br>
<br>
Please note the the last two series (24 & 25) inside the
container are label/macro images and I hence left them out.</p>
<p>If you check the original metadata then indeed it seems that the
information about the tile positions are missing. <br>
</p>
<p>However, the tile position is stored properly in the ome-xml
metadata.<br>
</p>
<p>As always thanks for your help and cheers,<br>
Kai<br>
</p>
<pre class="moz-signature" cols="72">--
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch">www.microscopynetwork.unibas.ch</a></pre>
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