Hi Nick,<br><br>I will second Will's suggestion to try the latest Bio-Formats trunk build (in addition to the link Will sent, it is also linked directly from the Bio-Formats download page: <a href="http://www.loci.wisc.edu/ome/formats-download.html">http://www.loci.wisc.edu/ome/formats-download.html</a>). In particular, you should no longer receive the error message about SamplesPerPixel with that build.<br>
<br>However, there is still a critical bug in the Bio-Formats Exporter. The problem is basically that the OME-XML block from the imported data gets fed directly to the exporter, when doing so is not always appropriate. There are times when some of the metadata has changed (e.g., the image has been cropped) and the OME-XML values need to be updated.<br>
<br>For more information, feel free to browse the ticket:<br> <a href="https://skyking.microscopy.wisc.edu/trac/java/ticket/405">https://skyking.microscopy.wisc.edu/trac/java/ticket/405</a><br><br>For now, here is a working macro to generate some compressed OME-TIFF files from the MRI Stack example dataset:<br>
<br>dir = getDirectory("Choose output directory");<br>run("MRI Stack (528K)");<br>run("Save", "save="+dir+"/mri-stack.tif");<br>close();<br>run("Bio-Formats Importer", "open="+dir+"/mri-stack.tif view=Hyperstack stack_order=XYCZT");<br>
run("Bio-Formats Exporter", "save="+dir+"/mri-stack-lzw.ome.tif compression=LZW");<br>run("Bio-Formats Exporter", "save="+dir+"/mri-stack-j2k.ome.tif compression=J2K");<br>
run("Bio-Formats Exporter", "save="+dir+"/mri-stack-j2k-lossy.ome.tif compression=J2K-Lossy");<br>run("Bio-Formats Exporter", "save="+dir+"/mri-stack-jpeg.ome.tif compression=JPEG");<br>
close();<br><br>Here is a file size comparison:<br>1,138,427 mri-stack.tif<br>654,514 mri-stack-lzw.ome.tif<br>422,370 mri-stack-j2k.ome.tif<br>275,379 mri-stack-j2k-lossy.ome.tif<br>144,257 mri-stack-jpeg.ome.tif<br><br>
-Curtis<br><br><div class="gmail_quote">On Tue, Sep 8, 2009 at 3:38 AM, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</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;">
<div style="word-wrap: break-word;">
Hi Nick,<div><br></div><div> One more thing to try, just to use the latest build of Bio-Formats.</div><div>You can get this from our automated build site. For LOCI this is</div><div><br></div><div><a href="http://hudson.openmicroscopy.org.uk/job/LOCI/" target="_blank">http://hudson.openmicroscopy.org.uk/job/LOCI/</a></div>
<div><br></div><div>Grab the latest loci_tools.jar there and put in ImageJ plugins folder etc...</div><div><br></div><div> Let us know if that helps. </div><div>If not, could you send any error message you get when exporting from ImageJ fails?</div>
<div><br></div><div> Cheers,</div><div><br></div><font color="#888888"><div> Will. </div></font><div><div></div><div class="h5"><div><br></div><div> </div><div><br><div><div>On 8 Sep 2009, at 09:31, Nick Perry wrote:</div>
<br><blockquote type="cite">Nope, I gave up.<br><br>Nick<br><br><div class="gmail_quote">On Tue, Sep 8, 2009 at 10:29 AM, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</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;"> <div style="word-wrap: break-word;"> Hi Nick,<div><br></div><div> I just tried this yesterday and also failed to export from ImageJ with Bioformats. (Don't remember the error I'm afraid). </div>
<div>However, I tried again today (possibly with different images) and it seems to be working OK (no errors).</div> <div><br></div><div>Hopefully you've got this to work now? </div><div><br></div><div> Will. </div>
<div>
<br></div><div><br><div><div><div></div><div><div>On 7 Sep 2009, at 08:12, Nick Perry wrote:</div><br> </div></div><blockquote type="cite"><div><div></div><div>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" target="_blank">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;">
<div link="blue" vlink="purple" lang="EN-US"> <div><p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Nick,</span></p><div><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span><br></div><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>
<div><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span><br></div><p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Best,</span></p><div><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span><br>
</div><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><p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">Research Investigator</span></p>
<div><span style="font-size: 10.5pt; color: rgb(31, 73, 125);"> </span><br></div><p><b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">G</span></b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">enomic Institute of the</span></p>
<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><p><b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">F</span></b><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">oundation</span></p>
<p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">Department of Informatics, room C117</span></p><p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">10675 John Jay Hopkins Drive</span></p><p><span style="font-size: 10.5pt; color: rgb(31, 73, 125);">San Diego CA 92121</span></p>
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<div><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span><br></div> <div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0mm 0mm;">
<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>
</div><div><div></div><div><div> <br></div><p>Hi Nick,</p> <div><div> <br></div> </div> <div><p>You can generate one using the Bio-Formats Exporter plugin for ImageJ.</p> </div> <div><div> <br></div> </div> <div><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>
</div> <div><div> <br></div> </div> <div><p>-Curtis</p> </div> <div><div> <br></div> <div><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> _______________________________________________<br> ome-devel mailing list<br> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
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William Moore</div><div><div style="margin: 0px;">Division of Gene Regulation and Expression</div><div style="margin: 0px;">College of Life Sciences</div><div style="margin: 0px;">University of Dundee</div><div style="margin: 0px;">
Scotland</div><div style="margin: 0px;">DD1 5PH</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Tel 01382 386364</div></div></span> </div><br></div></div></blockquote></div><br><div style="margin: 0px;">
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William Moore</div><div><div style="margin: 0px;">Division of Gene Regulation and Expression</div><div style="margin: 0px;">College of Life Sciences</div><div style="margin: 0px;">University of Dundee</div><div style="margin: 0px;">
Scotland</div><div style="margin: 0px;">DD1 5PH</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Tel 01382 386364</div></div></span> </div><br></div></div></div></div><br>_______________________________________________<br>
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