[ome-users] Handling tiled images

[Melissa Linkert]

Hi Rob,

> Okay. Like I mentioned to Roger, I can provide sample images. One 4GB and another higher resolution of 12GB.
> 

I am sending information on how to FTP files to the OME team in a
private mail.  Once we have both datasets, it will be much easier to
assess which additional pieces of metadata can be populated.

Regards,
-Melissa

On Wed, Jul 31, 2013 at 07:38:57PM +0000, Robert Schuler wrote:
> 
> On Jul 31, 2013, at 12:21 PM, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>>
>  wrote:
> 
> 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
> 
> 
> Great. I will definitely look into that.
> 
> > 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?
> 
> No, there is no "StageLabel" in the metadata either.
> 
> If it has neither Plane/Position[XYZ], nor StageLabel, then it is a limitation of the Bio-Formats metadata conversion which we should fix.
> 
> Okay. Like I mentioned to Roger, I can provide sample images. One 4GB and another higher resolution of 12GB.
> 
> Thanks,
> 
> Rob
> 
> 
> 
> On Wed, Jul 31, 2013 at 2:09 PM, Robert Schuler <schuler at isi.edu<mailto:schuler at isi.edu>> wrote:
> 
> On Jul 31, 2013, at 2:27 AM, Roger Leigh <r.leigh at dundee.ac.uk<mailto: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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