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

[David Gault (Staff)]

Hi Kai,

Thank you for reporting the issue and providing sample data.
I was able to test and reproduce the problem as you reported. The basic ‘Stitch Tiles’ option available on the Bio-Formats plugins importer window will try to automatically stitch tiles were every series in the image is a tile and contains the same dimensions. In this particular case the file contains a label and macro image also which means that the basic option will not work in this case. This is perhaps something that the option could be smarter at handling in the future.

There is also a specific option on the CZI reader which should auto stitch tiles when being read however in this instance it does not appear to have worked.
https://docs.openmicroscopy.org/bio-formats/5.6.0/formats/options.html

Why this failed to work will require further investigation so I have opened a Trello card on the Bio-Formats inbox to follow up on it:
https://trello.com/c/7MRDBwSn/178-czi-file-not-automatically-stitching

With Thanks,
David Gault

On 15 Aug 2017, at 14:35, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:


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<smb://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<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

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