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Hi Again Gary
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<div>Good to know that you’ve found a solution. However, I find it puzzling that the files are different sizes.</div>
<div>We had a problem where bio-formats was writing multiple copies of the xml when called from Matlab.</div>
<div>The work-around was to add the following line:</div>
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<span style="color: rgb(0, 0, 0);">java.lang.System.setProperty(</span>'javax.xml.transform.TransformerFactory'<span style="color: rgb(0, 0, 0);">, </span>'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’<span style="color: rgb(0, 0, 0);">);</span></div>
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<span style="color: rgb(0, 0, 0);">to the Matlab code as in the example that I sent.</span></div>
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<span style="color: rgb(0, 0, 0);">Perhaps this might help.</span></div>
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<span style="color: rgb(0, 0, 0);">Regards</span></div>
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<span style="color: rgb(0, 0, 0);">Ian </span></div>
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<div>On 27 Oct 2014, at 12:43, Yellen, Gary <<a href="mailto:gary_yellen@hms.harvard.edu">gary_yellen@hms.harvard.edu</a>> wrote:</div>
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<span style="color: rgb(31, 73, 125);">I was able to solve both the OME-TIFF export speed problem and the ModuloAlongT problem by using a hybrid approach: using the LOCI tools to create the OME-XML metadata, but then using the MATLAB Tiff() class for the actual
OME-TIFF writing. I tried this because of information on the forums that the MicroManager saving of OME-TIFFs was faster than the Bio-formats code.<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125);">I’ve enclosed the MATLAB code that I used for this hybrid approach, in case anyone is interested. The first section is a little parochial (using our local data objects), but most of the code should be re-usable. This
code wrote a medium-sized set of data in 1.3 seconds, compared with 89 seconds for using only calls to LOCI for the writing; although both cases had BigTiff and LZW compression set, the file using the hybrid approach was also about ~3x smaller for some reason
(1.7 GB vs 5.3 GB; the 1.7 GB is essentially the same size as the MATLAB .mat file version of the same data). Both versions of the file are readable using the Bio-Formats importer in Fiji.<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125);">I have used simpler metadata notations for the TiffData entries; they just include the starting IFD number and the number of planes.<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125);">This also solved the problem with the ModuloAlongT SA metadata (which apparently became corrupted during or after the writer.saveBytes calls).<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125);">gary<o:p></o:p></span></div>
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<span><dF_saveAsOMETiff.m></span>_______________________________________________<br>
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