[ome-users] Handling tiled images

[Curtis Rueden]

Hi Robert & Roger,

> I'm unaware of ImageJ currently being able to do that.
> In the past, I've used the stitching plugin to stitch the separate
> images into a single big image.

Yes, Fiji has image stitching plugins that use Bio-Formats to extract
OME-XML metadata stage positions (and/or stage labels) in order to stitch
multiple tiles together.

See these pages for details:
* http://fiji.sc/Image_Stitching
* http://loci.wisc.edu/software/fiji-image-stitching

> So I do not get the PositionX, Y, Z attributes of the Plane, that I could
use to stitch the images together.

Does your data have StageLabel metadata then? If it has neither
Plane/Position[XYZ], nor StageLabel, then it is a limitation of the
Bio-Formats metadata conversion which we should fix.

Regards,
Curtis


On Wed, Jul 31, 2013 at 2:09 PM, Robert Schuler <schuler at isi.edu> wrote:

>
> On Jul 31, 2013, at 2:27 AM, Roger Leigh <r.leigh at dundee.ac.uk> wrote:
>
> > On 30/07/2013 18:50, Robert Schuler wrote:
> >> I am having trouble figuring out how to handle large tiled images with
> Bio-Formats 5, OMERO 5, and ImageJ 2 (using Bio-Formats 5). The input
> format is Zeiss CZI coming from a new Zeiss Axio Scan.Z1.
> >>
> >> It seems in all cases to treat the tiles as any other series of images,
> and in my test image there are some 423 series. It could very well be that
> I don't know what I'm doing...
> >>
> >> In OMERO5, when uploading the image, it expands it to 423 images. Also,
> when trying to open any of those images, it says the image is corrupt, so
> maybe some trouble handling the pixel data.
> >
> > It's possible, but whether this is a problem with Bio-Formats or OMERO
> > isn't possible to determine without having a sample image to investigate
> > further.  Would it be possible to upload an image demonstrating this
> > problem using http://qa.openmicroscopy.org.uk/qa/upload/ ?
>
> I can share the image but it is >4GB and the upload limit is 2GB. I could
> put it on a server here and you could pull it if that works for you.
>
> >
> >> In ImageJ2, when importing using the loci tools plugin (release 5), it
> asks which of the 423 images I want to open. So I cannot really view the
> whole image this way.
> >
> > This is a  limitation of the current OME data model,
>
> If I understand correctly the latest OME data model was released June
> 2013? And so with the latest data model, we should still expect to get
> tiles as separate image series, correct?
>
> > where tiles are
> > separate "images" in the XML, since each Image is essentially limited to
> > x/y/c/z/t dimensions.  However, each image does contain the positional
> > information which would enable a viewer to visualise the tiles together
> > as a whole; but I'm unaware of ImageJ currently being able to do that.
>
> Does the OMERO web viewer support this, if ImageJ does not?
>
> > In the past, I've used the stitching plugin to stitch the separate
> > images into a single big image.
>
> I would like to do this. However, I am not seeing the position metadata.
> For instance, after bfconvert'ing the czi to ome.tif and then dumping the
> ome xml using tiffcomment tool, I can get just this for each image:
>
>    <Image ID="Image:0" Name="ip-test-file.czi #1">
>
>       …snipped many other lines here…
>
>          <Plane ExposureTime="20.0" TheC="0" TheT="0" TheZ="0"/>
>          <Plane ExposureTime="20.0" TheC="1" TheT="0" TheZ="0"/>
>          <Plane ExposureTime="8.0" TheC="2" TheT="0" TheZ="0"/>
>       </Pixels>
>    </Image>
>
> So I do not get the PositionX, Y, Z attributes of the Plane, that I could
> use to stitch the images together. Is this not supported yet for CZI images?
>
> Thanks!
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