<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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'>Hi Sebastian,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I’m happy to share the code. My thought was that the OMETiffWriter_gy class (only has my initials because OMETiffWriter is such a general name) should actually be generally usable code, even though the other m file is more specific. I’m sure it would only cover a subset of applications, of course.<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'>I like your idea of providing a more simple interface through the helper methods. The reason I implemented my methods as part of a class object is because it can retain persistent state information about (e.g.) the next available annotation IDs in specific types. I find it useful to have the annotation IDs specify the type (e.g. Annotation:C0, Annotation:D3), as this makes de-referencing them much easier when the file is read back.<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'>I also meant to ask: some of the setXxxxAnnotationRef methods require an annotation index as well as the ID, but I’m not sure why this is necessary, as the ID seems to be a unique identifier.<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'>I am happy with my current hybrid solution – it seems to work quite efficiently. I have also created an OMETiffReader_gy class for reading back the series efficiently into MATLAB objects (and also reading back the metadata into a MATLAB structure). I have also subclassed both the reader and the writer objects to provide functions more specific to my own application (such as combining read metadata and image data back into a data object). I think that the general superclass and specific subclass might be a good approach for MATLAB users who want to read and write OME-TIFFs from their own applications.<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'>I’m sure you will still want to investigate the Bio-Formats performance, but there is no rush for my own purposes.<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'>Best regards,<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><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"'> Sebastien Besson [mailto:s.besson@dundee.ac.uk] <br><b>Sent:</b> Monday, November 03, 2014 10:15 AM<br><b>To:</b> Yellen, Gary<br><b>Cc:</b> OME-devel OME; Copeland, Jay Arnold Jesse<br><b>Subject:</b> Re: [ome-devel] MATLAB Class for fast and simple writing of OME-TIFFs<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Gary, <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>thank you very much for your email. <o:p></o:p></p></div><div><p class=MsoNormal>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<o:p></o:p></p></div><div><p class=MsoNormal>quite specific to your application but there are many methods useful for the community and it is really nice to see<o:p></o:p></p></div><div><p class=MsoNormal>concrete examples of usage.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>A couple of immediate thoughts:<o:p></o:p></p></div><div><div><p class=MsoNormal>- are you happy with your current hybrid solution? The performance issue arising with Bio-Formats only calls is<o:p></o:p></p></div><div><p class=MsoNormal> certainly something we want to investigate but this will require a bit of time. Having access to the code allows us<o:p></o:p></p></div></div><div><p class=MsoNormal> to schedule this in our agenda thought.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>- I am considering porting back some of this code back to the open-source code. In particular the mechanisms<o:p></o:p></p></div><div><p class=MsoNormal> for creating and linking annotations to images could likely be simplified for others by adding helper methods, e.g.<o:p></o:p></p></div><div><p class=MsoNormal> something like:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>>> tagID = createTagAnnotation(metadata, value); <o:p></o:p></p></div><div><div><p class=MsoNormal>>> linkImageAnnotation(metadata, imageIndex, tagID); <o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Would that be acceptable for you and if so do you have any comments/suggestions?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks again for sharing your code,<o:p></o:p></p></div><div><p class=MsoNormal>Sebastien<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 31 Oct 2014, at 21:09, Yellen, Gary <<a href="mailto:gary_yellen@hms.harvard.edu">gary_yellen@hms.harvard.edu</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi all –</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Please let me know if you find bugs in the OMETiffWriter_gy code, or if you make improvements.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>Best,</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gary</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span lang=DE style='font-size:8.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span lang=DE style='font-size:8.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gary Yellen, PhD :: Professor of Neurobiology</span><o:p></o:p></p></div><div><p class=MsoNormal><span lang=DE style='font-size:8.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Harvard Medical School :: 220 Longwood Ave [WAB 328] :: Boston, MA 02115</span><o:p></o:p></p></div><div><p class=MsoNormal><span lang=DE style='font-size:8.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>617-432-0137 :: <a href="mailto:gary_yellen@hms.harvard.edu"><span style='color:purple'>gary_yellen@hms.harvard.edu</span></a></span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><OMETiffWriter_gy.m><dF_saveAsOMETiff.m><o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Dr Sébastien Besson<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Open Microscopy Environment / Harvard Medical School<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Wellcome Trust Centre for Gene Regulation and Expression,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>College of Life Sciences, University of Dundee, Dow Street,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Dundee DD1 5EH Scotland UK Tel: (01382) 386364<o:p></o:p></span></p></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><br><span style='font-size:10.0pt'>The University of Dundee is a registered Scottish Charity, No: SC015096</span> <o:p></o:p></p></div></body></html>