[ome-users] Position of scenes in CZI files

[David Gault (Staff)]

Hi Nicholas,

I have been able to take a look at the submitted file and can see the metadata values that you mentioned. Typically Bio-Formats always works with positions from the top left of the image so these Centre Position metadata values are not ones which we have parsed before.

Taking a look at the PositionX and PositionY values on the Plane and these have a unit of ReferenceFrame which is not what I would have expected. There was a fix recently to improve the parsing of these values which included updating the units to micron https://github.com/openmicroscopy/bioformats/pull/2881. Comparing it to the CenterPosition from the global metadata and I too am unsure exactly how this value relates or what units it is in (my guess would also have been microns). I have opened a card on the Bio-Formats Trello inbox (https://trello.com/c/x5ihZ1WS/163-czi-positionx-and-positiony-values) to follow up and continue this investigation to ensure that the position values are being populated correctly here.

With Thanks,
David Gault

On 24 Jul 2017, at 11:11, Nick Trahearn <nick.trahearn at icr.ac.uk<mailto:nick.trahearn at icr.ac.uk>> wrote:

Hi,

Thanks for your response. I've just had a quick look through the code-blocks you referred me to. Unfortunately, it seems that setPlanePositionX (and the others) are only being called three times per image (once for the first series, plus once for the barcode and preview image series at the end of the set).

I should mention there is something to do with position in the global metadata, stored under the key "Information|Image|S|Scene|CenterPosition #N" (where N is the index of the series). The issue is that this value doesn't appear to be in pixels. I assumed that it might be microns, but attempts to convert it into pixels using the microns/pixel resolution of the scanner gave me equally strange values.

I tried to provide a sample file at the link you provided, but unfortunately I'm getting an "Upload Error: 413". If there's an alternative way of uploading files please let me know.

All the best.
Nicholas Trahearn.
________________________________________
From: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] on behalf of Balaji Ramalingam (Staff) [b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>]
Sent: 21 July 2017 17:04
To: OME User Support List
Subject: Re: [ome-users] Position of scenes in CZI files

Hi,

Thank you for sharing your issue.

Please take a look at the following code-blocks from the Bio-Formats CZI reader,

The stage positions are being read under certain conditions,
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1228
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1240
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1252

And
The series/scene information is being read under certain conditions as well,
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1153

Could you please submit a sample file to the following link,
https://www.openmicroscopy.org/qa2/qa/upload/

This would help us troubleshoot your issue in better detail.
Thank you,

Best,
Balaji


On 20/07/2017, 15:32, "ome-users on behalf of Nick Trahearn" <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of nick.trahearn at icr.ac.uk<mailto:nick.trahearn at icr.ac.uk>> wrote:

   Dear All,

   Recently I've been working with CZI images using BioFormats. I'm not overly familiar with the format and its various forms but, in the images I have, each detected tissue section is placed into its own separate series (or scene, as they are called in Zeiss' viewer). I want to be able to stitch series together, relative to their original positions on the slide, in order to turn these individual sections back into a continuous image. Most of the tools required to do this are already available within BioFormats' ZeissCZIReader, but, as far as I can tell, there isn't a way to get the relative position of a series. It would be reasonably easy to add this into the existing reader, requiring just a few small additions, but I wanted to ensure that I hadn't missed anything obvious before I opened a pull request.

   All the best.
   Nicholas Trahearn.

   The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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