Hi Richard,<br><br><br><blockquote style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">I installed the stitching plugins to which you sent me the link.
However, when I follow the procedure you mentioned, I get an error that
says "Exception: null / Could not initialise stitching." In order to
attempt to stitch the image, I unchecked "Compute overlap," selected
"Save computation time (but use more RAM)" (we have 192GB of RAM), and
all other settings were defaults.<div> </div>Are there any further pointers you could give me in order to avoid this error?<br></blockquote>
<br>Your best bet is to seek help on the fiji-users list, since the Stitching plugins are part of Fiji.<br><br>I have CCed that list, in hopes that someone can help you out.<br><br>Regards,<br>Curtis<br><br><br><div class="gmail_quote">
On Mon, Apr 16, 2012 at 8:29 AM, Richard Lipkin <span dir="ltr"><<a href="mailto:lipkinr@nyspi.columbia.edu">lipkinr@nyspi.columbia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Dear Melissa,</div><div> </div><div>Thanks very much for the information. I installed the stitching plugins to which you sent me the link. However, when I follow the procedure you mentioned, I get an error that says "Exception: null / Could not initialise stitching." In order to attempt to stitch the image, I unchecked "Compute overlap," selected "Save computation time (but use more RAM)" (we have 192GB of RAM), and all other settings were defaults.</div>
<div> </div><div>Are there any further pointers you could give me in order to avoid this error?<br></div><div>Thanks very much again,</div><div> </div><div>Richard<br><br></div><div class="gmail_quote">On Thu, Apr 12, 2012 at 2:57 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">Hi Richard,<div class="im"><br>
<div><br>
> I am writing from Andrew Dwork's lab at Columbia University. I was very<br>
> pleased to see that your latest version of LOCI provides support for the<br>
> Carl Zeiss .czi imaging format. However, I have run into a minor snag while<br>
> importing images, and I was wondering whether you can provide some advice.<br>
><br>
> I have some .czi images that each contain numerous stacks stitched together<br>
> in specific relationships to one another. When I run the LOCI bio-formats<br>
> importer, it gives me a choice of which of these stacks to open. It then<br>
> lets me choose which dimension gets which planes (Z, C, or T). Then it<br>
> opens the individual stacks flawlessly. My question is, is it possible to<br>
> have LOCI import these .czi files as one big image with the stitching<br>
> between the stacks preserved?<br>
<br>
</div></div><div class="im">Yes - there are two options for doing so. To get a very rough stitched<br>
image, you can select the "Stitch tiles" option in the "Bio-Formats<br>
Import Options" window. This will attempt to stitch the stacks back<br>
together based upon the stage positions, but it assumes 0% overlap<br>
(which more often than not is not the case).<br>
<br>
The much better solution is to use the stitching plugins developed by<br>
Stephan Preibisch:<br>
<br>
<a href="http://fiji.sc/wiki/index.php/Image_Stitching" target="_blank">http://fiji.sc/wiki/index.php/Image_Stitching</a><br>
<br>
...which will open the file for you (using Bio-Formats) and perform the<br>
stitching based upon the metadata in the file and some parameters that<br>
you specify.<br>
<br>
In this case, you probably want to use it by selecting<br>
"Plugins > Stitching > Grid/Collection stitching", then set the type to<br>
"Positions from file" and the order to "Defined by image metadata".<br>
You'll then be asked for the name of the file and some extra parameters,<br>
after which point the stitched image should just appear.<br>
<br>
Regards,<br>
-Melissa<br>
</div><div><div><div class="im"><br>
On Thu, Apr 12, 2012 at 09:53:03AM -0400, Richard Lipkin wrote:<br></div><div><div class="h5">
> Dear OME Users list,<br>
><br>
> I am writing from Andrew Dwork's lab at Columbia University. I was very<br>
> pleased to see that your latest version of LOCI provides support for the<br>
> Carl Zeiss .czi imaging format. However, I have run into a minor snag while<br>
> importing images, and I was wondering whether you can provide some advice.<br>
><br>
> I have some .czi images that each contain numerous stacks stitched together<br>
> in specific relationships to one another. When I run the LOCI bio-formats<br>
> importer, it gives me a choice of which of these stacks to open. It then<br>
> lets me choose which dimension gets which planes (Z, C, or T). Then it<br>
> opens the individual stacks flawlessly. My question is, is it possible to<br>
> have LOCI import these .czi files as one big image with the stitching<br>
> between the stacks preserved?<br>
><br>
> Thank you very much for your assistance,<br>
><br>
> Richard Lipkin<br>
> <a href="mailto:lipkinr@nyspi.columbia.edu" target="_blank">lipkinr@nyspi.columbia.edu</a><br>
<br>
</div></div></div></div><div class="im">> _______________________________________________<br>
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