<div dir="ltr">Hi Robert & Roger,<div><br></div><div>> <span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">I'm unaware of ImageJ currently being able to do that.</span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">> In the past, I've used the stitching plugin to stitch the separate</span><br style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">
<span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">> images into a single big image.</span><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">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.</span></div>
<div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">See these pages for details:</span></div>
<div><font color="#500050" face="arial, sans-serif">* <a href="http://fiji.sc/Image_Stitching">http://fiji.sc/Image_Stitching</a></font><br></div><div><font color="#500050" face="arial, sans-serif">* <a href="http://loci.wisc.edu/software/fiji-image-stitching">http://loci.wisc.edu/software/fiji-image-stitching</a><br>
</font></div><div><font color="#500050" face="arial, sans-serif"><br></font></div><div><font color="#500050" face="arial, sans-serif">> </font><span style="font-family:arial,sans-serif;font-size:13px">So I do not get the PositionX, Y, Z attributes of the Plane, that I could use to stitch the images together.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">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.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><font color="#500050" face="arial, sans-serif">Regards,</font></div><div><font color="#500050" face="arial, sans-serif">Curtis</font></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jul 31, 2013 at 2:09 PM, Robert Schuler <span dir="ltr"><<a href="mailto:schuler@isi.edu" target="_blank">schuler@isi.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
On Jul 31, 2013, at 2:27 AM, Roger Leigh <<a href="mailto:r.leigh@dundee.ac.uk">r.leigh@dundee.ac.uk</a>> wrote:<br>
<br>
> On 30/07/2013 18:50, Robert Schuler wrote:<br>
>> 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.<br>
>><br>
>> 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...<br>
>><br>
>> 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.<br>
><br>
> It's possible, but whether this is a problem with Bio-Formats or OMERO<br>
> isn't possible to determine without having a sample image to investigate<br>
> further. Would it be possible to upload an image demonstrating this<br>
> problem using <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a> ?<br>
<br>
</div>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.<br>
<div class="im"><br>
><br>
>> 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.<br>
><br>
> This is a limitation of the current OME data model,<br>
<br>
</div>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?<br>
<div class="im"><br>
> where tiles are<br>
> separate "images" in the XML, since each Image is essentially limited to<br>
> x/y/c/z/t dimensions. However, each image does contain the positional<br>
> information which would enable a viewer to visualise the tiles together<br>
> as a whole; but I'm unaware of ImageJ currently being able to do that.<br>
<br>
</div>Does the OMERO web viewer support this, if ImageJ does not?<br>
<div class="im"><br>
> In the past, I've used the stitching plugin to stitch the separate<br>
> images into a single big image.<br>
<br>
</div>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:<br>
<br>
<Image ID="Image:0" Name="ip-test-file.czi #1"><br>
<br>
…snipped many other lines here…<br>
<br>
<Plane ExposureTime="20.0" TheC="0" TheT="0" TheZ="0"/><br>
<Plane ExposureTime="20.0" TheC="1" TheT="0" TheZ="0"/><br>
<Plane ExposureTime="8.0" TheC="2" TheT="0" TheZ="0"/><br>
</Pixels><br>
</Image><br>
<br>
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?<br>
<br>
Thanks!<br>
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