So I can't actually get the ImageJ plugin for bio-formats to actually work... Every time I import an image either with the LOCI tool or the standard ImageJ 'open' and try to export it, I get errors. I've tried playing around with the import options as well (splitting channels into separate images, etc). I've attached one of the error messages as an image. Anyone know how to actually get this to work..? I've tried opening .ome.tif files and a .jpg.<br>
<br>Nick<br><br><div class="gmail_quote">On Fri, Sep 4, 2009 at 6:15 PM, Ghislain Bonamy <span dir="ltr"><<a href="mailto:GBonamy@gnf.org">GBonamy@gnf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Nick,</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">I am sure you are aware of this, but though I would point this
out anyways. The JPEG200 compression is a lossless compression (not like
regular JPEG). The advantage of LZW over JPEG2000 is that the image can still
be read by other image readers. On the flip side JPEG2000 will give you much
better compression of your data (in particular if your data is complex), but
the image will only be correctly handled by Bio-Formats.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Best,</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">Ghislain Bonamy, PhD</span></p>
<p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">__________________________________________</span></p>
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<p><b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">N</span></b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">ovartis Research</span></p>
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<p><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-devel-bounces@lists.openmicroscopy.org.uk</a>
[mailto:<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-devel-bounces@lists.openmicroscopy.org.uk</a>] <b>On Behalf Of </b>Curtis
Rueden<br>
<b>Sent:</b> Friday, September 04, 2009 6:56 AM<br>
<b>To:</b> Nick Perry<br>
<b>Cc:</b> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b> Re: [ome-devel] Compression in OME-TIFF file?</span></p>
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<p> </p>
<p>Hi Nick,</p>
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<p> </p>
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<div>
<p>You can generate one using the Bio-Formats Exporter plugin
for ImageJ.</p>
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<p> </p>
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<p style="margin-bottom: 12pt;">First, open any image. Then
choose Plugins > LOCI > Bio-Formats Exporter, save as OME-TIFF format,
and a dialog box will appear allowing you to select the compression
type—give either "LZW" or "JPEG2000" a try.</p>
</div>
<div>
<p>The compression will change nothing about the embedded
OME-XML, only how the TIFF planes are stored in the file. And all OME-TIFF
compression is plane by plane (i.e., no compression over a 3D block of pixels).</p>
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<p> </p>
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<p>-Curtis</p>
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<p> </p>
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<p>On Fri, Sep 4, 2009 at 4:16 AM, Nick Perry <<a href="mailto:nperry@stanford.edu" target="_blank">nperry@stanford.edu</a>> wrote:</p>
<p style="margin-bottom: 12pt;">Hi,<br>
<br>
Does anyone know where I can download an example OME-TIFF file that is
compressed? I see on the LOCI site (<a href="http://www.loci.wisc.edu/ome/ome-tiff-data.html" target="_blank">http://www.loci.wisc.edu/ome/ome-tiff-data.html</a>)
that it is possible to compress the data in an OME-TIFF file, like with LZW for
example, and I'm trying to find out where in an OME-TIFF file the compression
is specified. (This all hinges of course on my intuition that it is the raw
image data that is compressed, and not the surrounding tiff structure/ome-xml
block.)<br>
<br>
Thanks,<br>
<span style="color: rgb(136, 136, 136);">Nick<br>
</span><br>
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<p> </p>
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