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Hi Gary,
<div><br>
</div>
<div>after a bit of debugging, the error should be solved by reinitializing the IFD state before </div>
<div>each call to TiffWriter.saveBytes(). This should be solved by either creating a new</div>
<div>IFD in each iteration of the loop or resetting its state with for instance:</div>
<div><br>
</div>
<div>
<div style="margin: 0px; font-size: 10px; font-family: Courier;"> ifd.clear();</div>
<div style="margin: 0px; font-size: 10px; font-family: Courier;"> ifd.putIFDValue(ifd.ROWS_PER_STRIP, szY);</div>
</div>
<div><br>
</div>
<div>Adding this two lines was enough to remove the Error thrown by running showinf on the</div>
<div>generated OME-TIFF files while preserving the size. I would expect this will also solve the</div>
<div>import into OMERO.</div>
<div><br>
</div>
<div>Could you try and let us know?</div>
<div>Sebastien</div>
<div><br>
</div>
<div><br>
<div>
<div>On 29 Oct 2014, at 20:57, Yellen, Gary <<a href="mailto:gary_yellen@hms.harvard.edu">gary_yellen@hms.harvard.edu</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Gary<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div>
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<b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"><span class="Apple-converted-space"> </span>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>Munro, Ian<br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, October 29, 2014 10:26 AM<br>
<b>To:</b><span class="Apple-converted-space"> </span>OME OME-devel<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation<o:p></o:p></span></div>
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<o:p> </o:p></div>
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Hi All<o:p></o:p></div>
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<o:p> </o:p></div>
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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></div>
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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></div>
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<o:p> </o:p></div>
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Reading pixel data (0-2)<o:p></o:p></div>
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Reading IFDs<o:p></o:p></div>
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Populating metadata<o:p></o:p></div>
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Error untangling IFDs; the OME-TIFF file may be malformed.<o:p></o:p></div>
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Error untangling IFDs; the OME-TIFF file may be malformed.<o:p></o:p></div>
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Read 3/3 planes (100%)<o:p></o:p></div>
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[done]<o:p></o:p></div>
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<o:p> </o:p></div>
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<o:p> </o:p></div>
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Is anyone else seeing this. I may have implemented the ifd mod incorrectly?<o:p></o:p></div>
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<o:p> </o:p></div>
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Regards<o:p></o:p></div>
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<o:p> </o:p></div>
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Ian <o:p></o:p></div>
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<o:p> </o:p></div>
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<o:p> </o:p></div>
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On 29 Oct 2014, at 12:44, Alexandrov, Yuriy <<a href="mailto:y.alexandrov@imperial.ac.uk" style="color: purple; text-decoration: underline;">y.alexandrov@imperial.ac.uk</a>> wrote:<o:p></o:p></div>
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<br>
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<o:p></o:p></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi All,</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Initialized and used exactly as Sebastien suggests -</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';"> ifd = loci.formats.tiff.IFD();</span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';"> ifd.putIFDValue(ifd.ROWS_PER_STRIP,sizeY);</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';">%% inside loop by “index”</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';">…</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';">writer.getWriter(ometiffilename).saveBytes(index-1, getBytes(I), ifd);</span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Courier New';">…</span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">So I switched to this method.</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Best,</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Y.</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></b><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"> </span></span><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">ome-devel
[<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;">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></div>
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<span lang="EN-GB"> <o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi Sebastien - Strange!</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">I just re-ran it:</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">First writing data with the hybrid Bio-Formats / Tiff() code...</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Elapsed time is 1.324383 seconds.</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Now writing data with all Bio-Formats code...</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Elapsed time is 5.011741 seconds.</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">java.lang.Runtime.getRuntime.maxMemory = 492175360</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Windows 7 SP1 x64</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Intel Core i7-4770 (3.40GHz)</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">MATLAB R2014a (64-bit)</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">gary</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></b><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"> </span></span><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">Sebastien
Besson [<a href="mailto:s.besson@dundee.ac.uk" style="color: purple; text-decoration: underline;"><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></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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HI Gary,<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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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></div>
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suggested changes, I have the following result:<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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>> gyTestScript<span lang="EN-GB"><o:p></o:p></span></div>
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First writing data with the hybrid Bio-Formats / Tiff() code...<span lang="EN-GB"><o:p></o:p></span></div>
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Elapsed time is 2.321489 seconds.<span lang="EN-GB"><o:p></o:p></span></div>
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Now writing data with all Bio-Formats code...<span lang="EN-GB"><o:p></o:p></span></div>
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Elapsed time is 2.448038 seconds.<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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and both generated OME TIFFs are about 1.5-1.6MB.<span lang="EN-GB"><o:p></o:p></span></div>
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Which version of MATLAB and which OS/architecture are you using?<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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Best,<span lang="EN-GB"><o:p></o:p></span></div>
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Sebastien<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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On 28 Oct 2014, at 17:27, Yellen, Gary <<a href="mailto:gary_yellen@hms.harvard.edu" style="color: purple; text-decoration: underline;"><span style="color: purple;">gary_yellen@hms.harvard.edu</span></a>> wrote:<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></p>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Thanks, Sebastien.</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Best,</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Gary</span><span lang="EN-GB"><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><span lang="EN-GB"><o:p></o:p></span></div>
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<b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></b><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"> </span></span><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">Sebastien
Besson [</span><a href="mailto:s.besson@dundee.ac.uk" style="color: purple; text-decoration: underline;"><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: purple;">mailto:s.besson@dundee.ac.uk</span></a><span style="font-size: 10pt; 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></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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Hi Gary,<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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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></div>
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the major difference between the whole Bio-Formats version and thelibTiff version is the following<span lang="EN-GB"><o:p></o:p></span></div>
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option:<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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tagstruct.RowsPerStrip = szY;<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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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></div>
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RowsPerStrip equal to the desired value, i.e.<span lang="EN-GB"><o:p></o:p></span></div>
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ifd = loci.formats.tiff.IFD();<span lang="EN-GB"><o:p></o:p></span></div>
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ifd.putIFDValue(ifd.ROWS_PER_STRIP, szY);<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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This object can then be passed to TiffWriter.saveBytes():<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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1- either if you initialize an ImageWriter() using<span lang="EN-GB"><o:p></o:p></span></div>
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writer.getWriter(fname).saveBytes(index, getBytes(plane(:)), ifd);<span lang="EN-GB"><o:p></o:p></span></div>
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2- or if you directly initialize an OMETiffWriter() using<span lang="EN-GB"><o:p></o:p></span></div>
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writer.saveBytes(index, getBytes(plane(:)), ifd);<span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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Locally adding this option brought your Bio-Formats code to similar levels of performance<span lang="EN-GB"><o:p></o:p></span></div>
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in terms of file size and writing time. <span lang="EN-GB"><o:p></o:p></span></div>
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<span lang="EN-GB"><o:p></o:p></span></div>
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Could you try this and let us know?<span lang="EN-GB"><o:p></o:p></span></div>
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Sebastien<span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\axis2\activation.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\shared\controllib.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\dastudio.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\rptgencore.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\testmeas.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\storage\gdsinmatlab.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\storage\provider.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\storage\motw.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\storage\filesystemadapter.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\activation.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\symbolic.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\toolbox\timeseries.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\webintegration.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\mlwebservices.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\net.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\webproxy.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\mwaws_client.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\dws_client.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\webservices\loginws_client.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\webservices\dws_client.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\webservices\ws_client_core\mw-service-client-core.jar<span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jarext\webservices\ws_usagedata_client\usagedata-client.jar<span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\activation_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\install_api_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\professional_activation_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\shared_install_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\student_activation_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Program Files\MATLAB\R2014a\java\jar\zh_CN\web_connectivity_res.jar <span lang="EN-GB"><o:p></o:p></span></div>
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C:\Users\Public\Documents\MATLAB\bioformats_package.jar <span lang="EN-GB"><o:p></o:p></span></div>
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DYNAMIC JAVA PATH<span lang="EN-GB"><o:p></o:p></span></div>
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<empty><span lang="EN-GB"><o:p></o:p></span></p>
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<span lang="EN-GB" style="font-size: 9pt; font-family: Helvetica, sans-serif;">_______________________________________________<br>
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</div>
</blockquote>
</div>
<br>
<div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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