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Hi Gary,
<div><br>
</div>
<div>thank you very much for your email. </div>
<div>Regarding the code itself, I had a quick glance at it and did not see any obvious issue so far. Obviously part of it is</div>
<div>quite specific to your application but there are many methods useful for the community and it is really nice to see</div>
<div>concrete examples of usage.</div>
<div><br>
</div>
<div>A couple of immediate thoughts:</div>
<div>
<div>- are you happy with your current hybrid solution? The performance issue arising with Bio-Formats only calls is</div>
<div> certainly something we want to investigate but this will require a bit of time. Having access to the code allows us</div>
</div>
<div> to schedule this in our agenda thought.</div>
<div><br>
</div>
<div>- I am considering porting back some of this code back to the open-source code. In particular the mechanisms</div>
<div> for creating and linking annotations to images could likely be simplified for others by adding helper methods, e.g.</div>
<div> something like:</div>
<div><br>
</div>
<div>>> tagID = createTagAnnotation(metadata, value); </div>
<div>
<div>>> linkImageAnnotation(metadata, imageIndex, tagID); </div>
</div>
<div><br>
</div>
<div>Would that be acceptable for you and if so do you have any comments/suggestions?</div>
<div><br>
</div>
<div>Thanks again for sharing your code,</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 31 Oct 2014, at 21:09, 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);">Hi all –<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);">Here is some code for exporting OME-TIFFs from MATLAB data, using a combination of Bio-Formats calls for the metadata and MATLAB Tiff calls for the actual file writing.
I have found the speed to be significantly faster than using all Bio-Formats calls.<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 also included tools (hopefully general!) for adding all different types of annotations to the images, without wrestling with the many Java calls necessary to do this.<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);">The main code is the OMETiffWriter_gy class, in a single file. There’s documentation of the workflow at the top of the code. I’ve also included example code in the dF_saveAsOMETiff.m
file, which is just for your perusal since it requires object classes that are peculiar to our lab.<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);">Please let me know if you find bugs in the OMETiffWriter_gy code, or if you make improvements.<o:p></o:p></span></div>
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Best,<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<o:p></o:p></span></div>
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<span lang="DE" style="font-size: 8pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Gary Yellen, PhD :: Professor of Neurobiology</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p></o:p></span></div>
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<span lang="DE" style="font-size: 8pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Harvard Medical School :: 220 Longwood Ave [WAB 328] :: Boston, MA 02115</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p></o:p></span></div>
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<span lang="DE" style="font-size: 8pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">617-432-0137 :: <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></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p></o:p></span></div>
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<span><OMETiffWriter_gy.m></span><span><dF_saveAsOMETiff.m></span></div>
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<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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