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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I finally got to try uploading my files to an OMERO server, and I see the same problem as Ian. The metadata import ok, but the images are no good and the Import Log is full of “Error untangling IFDs; the OME-TIFF file may be malformed” messages.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>OMERO can read the slow (70 sec to write) and oversized (5 MB instead of 1.6) file written with Bio-Formats just fine.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Fiji can read the hybrid file (Bio-Formats for metadata, MATLAB for Tiff writing) just fine, but OMERO has a number of problems with it – the nominally compliant use of a simplified <TiffData IFD=”0” PlaneCount=”90”> is not handled by OMERO, which seems to insist on have TheC etc. specified for every single plane.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gary<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> ome-devel [mailto:ome-devel-bounces@lists.openmicroscopy.org.uk] <b>On Behalf Of </b>Munro, Ian<br><b>Sent:</b> Wednesday, October 29, 2014 10:26 AM<br><b>To:</b> OME OME-devel<br><b>Subject:</b> Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi All<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>I’m just in the process of checking this to ensure that the data that is read back is the same both with and without this modification. <o:p></o:p></p><div><p class=MsoNormal>If I run the command line 'showinf tool 'on the smaller files produced with the suggested ifd mod then I get the following in the output:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>Reading pixel data (0-2)<o:p></o:p></p></div><div><p class=MsoNormal>Reading IFDs<o:p></o:p></p></div><div><p class=MsoNormal>Populating metadata<o:p></o:p></p></div><div><p class=MsoNormal>Error untangling IFDs; the OME-TIFF file may be malformed.<o:p></o:p></p></div><div><p class=MsoNormal>Error untangling IFDs; the OME-TIFF file may be malformed.<o:p></o:p></p></div><div><p class=MsoNormal>Read 3/3 planes (100%)<o:p></o:p></p></div><div><p class=MsoNormal>[done]<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Is anyone else seeing this. I may have implemented the ifd mod incorrectly?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Regards<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Ian <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 29 Oct 2014, at 12:44, Alexandrov, Yuriy <<a href="mailto:y.alexandrov@imperial.ac.uk">y.alexandrov@imperial.ac.uk</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi All,</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I checked how Sebastien’s method works on my (Win 7) machine – for my example 5 frame OPT data, it provides slightly smaller files (18M vs 20M) and works a bit faster (0.22 vs 0.34 s/frame). Frame is 1191x2559 uint16.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Initialized and used exactly as Sebastien suggests -</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ifd = loci.formats.tiff.IFD();</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ifd.putIFDValue(ifd.ROWS_PER_STRIP,sizeY);</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>%% inside loop by “index”</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>…</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>writer.getWriter(ometiffilename).saveBytes(index-1, getBytes(I), ifd);</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>…</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>So I switched to this method.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Y.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>ome-devel [<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</a>]<span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Yellen, Gary<br><b>Sent:</b><span class=apple-converted-space> </span>28 October 2014 19:33<br><b>To:</b><span class=apple-converted-space> </span>Besson, Sebastien (forwarding)<br><b>Cc:</b><span class=apple-converted-space> </span>OME-devel OME<br><b>Subject:</b><span class=apple-converted-space> </span>Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation</span><span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span lang=EN-GB> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Sebastien - Strange!</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I just re-ran it:</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>First writing data with the hybrid Bio-Formats / Tiff() code...</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Elapsed time is 1.324383 seconds.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Now writing data with all Bio-Formats code...</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Elapsed time is 5.011741 seconds.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>java.lang.Runtime.getRuntime.maxMemory = 492175360</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Windows 7 SP1 x64</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Intel Core i7-4770 (3.40GHz)</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>MATLAB R2014a (64-bit)</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I am getting a smaller filesize now with the Bio-Formats code: 1.57MB (might have had writer.close errors before that resulted in appending), but it still take 4.7 to 5 seconds.</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I wonder if it’s something related to the filesystem and file allocation/growth. My disk is only ~25% full, so shouldn’t be a big issue. I did just try both tests to an empty scratch directory; both were faster but I still see the difference (1.20 vs. 4.38 sec).</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Also – the bioformats_package.jar is at the end of my static java path, right after all the MATLAB .jars. (see below at the bottom of the email.) Could this be the issue?</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>gary</span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Sebastien Besson [<a href="mailto:s.besson@dundee.ac.uk"><span style='color:purple'>mailto:s.besson@dundee.ac.uk</span></a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, October 28, 2014 3:16 PM<br><b>To:</b><span class=apple-converted-space> </span>Yellen, Gary<br><b>Cc:</b><span class=apple-converted-space> </span>OME-devel OME<br><b>Subject:</b><span class=apple-converted-space> </span>Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation</span><span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal>HI Gary,<span lang=EN-GB><o:p></o:p></span></p></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>thanks for the heads up. Strangely, with the code you attached to your email which matches my<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>suggested changes, I have the following result:<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>>> gyTestScript<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>First writing data with the hybrid Bio-Formats / Tiff() code...<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Elapsed time is 2.321489 seconds.<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Now writing data with all Bio-Formats code...<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Elapsed time is 2.448038 seconds.<span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>and both generated OME TIFFs are about 1.5-1.6MB.<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Which version of MATLAB and which OS/architecture are you using?<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Best,<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Sebastien<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal>On 28 Oct 2014, at 17:27, Yellen, Gary <<a href="mailto:gary_yellen@hms.harvard.edu"><span style='color:purple'>gary_yellen@hms.harvard.edu</span></a>> wrote:<span lang=EN-GB><o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'> <span lang=EN-GB><o:p></o:p></span></p><div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks, Sebastien.</span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I found that this made some improvement: The time is now 4.66 sec (vs. previous 70 sec and alternate 1.26 sec), and the filesize is slightly improved (4.5 MB, vs previous 5.3 MB and alternate 1.65 MB).</span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I’ve enclosed the modified code, which includes my interpretation of your suggested changes (I created the new IFD only once, and then set owriter=writer.getWriter(fname)). Please let me know if this is not quite what you meant.</span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,</span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gary</span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span lang=EN-GB><o:p></o:p></span></p></div></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Sebastien Besson [</span><a href="mailto:s.besson@dundee.ac.uk"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:purple'>mailto:s.besson@dundee.ac.uk</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, October 28, 2014 12:25 PM<br><b>To:</b><span class=apple-converted-space> </span>Yellen, Gary<br><b>Cc:</b><span class=apple-converted-space> </span>OME-devel OME<br><b>Subject:</b><span class=apple-converted-space> </span>Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation</span><span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Hi Gary,<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>thanks for sending the code and some test data. After some debugging and with Melissa's input,<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>the major difference between the whole Bio-Formats version and thelibTiff version is the following<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>option:<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>tagstruct.RowsPerStrip = szY;<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>If writing using Bio-Formats, a workaround is to construct a loci.formats.tiff.IFD object with the<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>RowsPerStrip equal to the desired value, i.e.<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal>ifd = loci.formats.tiff.IFD();<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>ifd.putIFDValue(ifd.ROWS_PER_STRIP, szY);<span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>This object can then be passed to TiffWriter.saveBytes():<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>1- either if you initialize an ImageWriter() using<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> writer.getWriter(fname).saveBytes(index, getBytes(plane(:)), ifd);<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>2- or if you directly initialize an OMETiffWriter() using<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> writer.saveBytes(index, getBytes(plane(:)), ifd);<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Locally adding this option brought your Bio-Formats code to similar levels of performance<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>in terms of file size and writing time. <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Could you try this and let us know?<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal>Sebastien<span lang=EN-GB><o:p></o:p></span></p></div></div><div><div style='border:none;border-bottom:double windowtext 2.25pt;padding:0in 0in 1.0pt 0in'><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div></div></div><div><div><p class=MsoNormal><br> STATIC JAVA PATH<span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\patch <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\AnimatedTransitions.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ant.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ant-launcher.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\antlr.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\felix.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\scr.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\activation.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axiom-api.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axiom-impl.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-adb.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-kernel.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-transport-http.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\axis2-transport-local.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\commons-httpclient.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\geronimo-stax-api.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\httpcore.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\mail.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\neethi.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\wsdl4j.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\wstx-asl.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\axis2\XmlSchema.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-anim.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-extension.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-dom.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-transcoder.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-awt-util.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-bridge.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-gvt.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-css.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-parser.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-ext.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-gui-util.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-svggen.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-codec.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-svg-dom.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-script.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-util.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-swing.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\batik-xml.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\bluecove-bluez.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\bluecove-emu.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\bluecove.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\chilkat\chilkat.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-codec.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-collections-generic.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-collections.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-compress.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-io.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-lang.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-logging.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-math.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\commons-net.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\dom4j.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\emma_ant.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\emma.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\fop.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\avalon-framework.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\foxtrot.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\glazedlists_java15.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\google-collect.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\guice\aopalliance.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\guice\guice.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\guice\guice-assistedinject.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\guice\javax.inject.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\distcomp\h2.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ice.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ib6core.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ib6extra.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ib6http.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ib6https.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\ice\ib6js.jar <span 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class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\util.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\common.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\mwswing.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\beans.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\mwt.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\xml.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\desktop.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\toolstrip.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program 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lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jarext\webservices\ws_usagedata_client\usagedata-client.jar<span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\activation_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\install_api_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\professional_activation_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\shared_install_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\student_activation_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\web_connectivity_res.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> C:\Users\Public\Documents\MATLAB\bioformats_package.jar <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> DYNAMIC JAVA PATH<span lang=EN-GB><o:p></o:p></span></p></div><div><p class=MsoNormal> <span lang=EN-GB><o:p></o:p></span></p></div><p class=MsoNormal style='margin-bottom:12.0pt'> <empty><span lang=EN-GB><o:p></o:p></span></p></div></div></div><p class=MsoNormal><span lang=EN-GB style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>_______________________________________________<br>ome-devel mailing list<br><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> 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