[ome-users] Position of scenes in CZI files

[Melissa Linkert]

Hi Nicholas,

> 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.

Alternate instructions for sending files to the OME team have now been
sent to you by private email.

Regards,
-Melissa

On Mon, Jul 24, 2017 at 5:11 AM, Nick Trahearn <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] on behalf of Balaji Ramalingam (Staff) [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 on behalf of 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.
>
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