[ome-users] Axioscan *.czi stage positions not recognised?

[Kai Schleicher]

Hi OME team,

I ran into an issue with a Zeiss *.czi produced by the Axioscan 
Slidescanner. This dataset (download, 530 MB 
<https://filesender.switch.ch/filesender/?vid=26acedaa-f108-7348-ca3a-00006ae0f68d>) 
contains:
1 scene, 23 unstitched tiles 2040 x 2040 , 2 channels , 3 z , 1 overview 
and 1 label image

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.

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?

Here is what I tried:

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");

Please note the the last two series (24 & 25) inside the container are 
label/macro images and I hence left them out.

If you check the original metadata then indeed it seems that the 
information about the tile positions are missing.

However, the tile position is stored properly in the ome-xml metadata.

As always thanks for your help and cheers,
Kai

-- 
>>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) | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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