<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div>
<div style="color: rgb(34, 34, 34); widows: 1; background-color: rgb(255, 255, 255);">
Dear Sho,</div>
<div style="color: rgb(34, 34, 34); widows: 1; background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="color: rgb(34, 34, 34); widows: 1; background-color: rgb(255, 255, 255);">
Yes, several people have contacted us about 3D HISTECH .mrxs. At the moment, the complexity of the format, and as noted below, the work we need to do to deliver a complete solution for the format means that we have to lower its priority. I'm afraid I cannot
give you an ETA. My understanding is that you are already CC'd on the Trac ticket that records any milestone progress on the implementation:</div>
<span class="im" style="widows: 1; background-color: rgb(255, 255, 255);">
<div>
<div style="color: rgb(80, 0, 80);"><br>
</div>
<div style="color: rgb(80, 0, 80);"> <a href="http://trac.openmicroscopy.org/ome/ticket/4121" rel="noreferrer" target="_blank" style="color: rgb(17, 85, 204);">http://trac.<wbr>openmicroscopy.org/ome/ticket/<wbr>4121</a></div>
<div style="color: rgb(80, 0, 80);"><br>
</div>
<div>I can assure you that this is the best way to be notified if the priority changes or there is development of note.</div>
</div>
<div><br>
</div>
</span><span class="im" style="widows: 1; background-color: rgb(255, 255, 255);">
<div><font>A few more details</font>:<font> we haven’t deliver</font>ed a full reader for .mrxs, and there hasn’t been substantial public development, but we have spent a great deal of time examining the format and potential solutions, and building test readers.
So we know a lot about this format. W<font>e can say with some confidence that the 3D HISTECH .mrxs file format is the most complex whole slide imaging file format we have ever encountered.</font><font> Thanks to the example data the community has generously
provided, we have been able to analyse the on disk layout as well as the compression types and map out the details of what an implementation would entail.</font></div>
<div style="color: rgb(80, 0, 80);"><br>
</div>
<div style="color: rgb(80, 0, 80);"><font color="#222222">One thing to understand about our work, strategy and commitment for supporting all file formats, especially formats used in production-scale facilities that use tech like whole slide imaging, is that
we insist on delivering as close to complete support as possible.</font> <font color="#222222">This is important given the size of community we support, the breadth of applications that use our software, and the need for utility and reliability in the software
we deliver to the community. With .mrxs, it is very hard and expensive to meet this goal. To be specific:</font></div>
</span>
<ul>
<li><font color="#222222">The design decisions of 3D HISTECH with respect to image pyramid layout are at odds with what we can reasonably handle within the infrastructure currently in place. Our analysis suggests we will have to re-calculate several of the
resolution levels, because of choices 3D HISTECH has made in their tiling strategy. This will create a substantial performance penalty for anyone using Bio-Formats to read this format.</font></li><li><font color="#222222" style="widows: 1;">The strategy for storing binary data on disk in</font><span style="color: rgb(80, 0, 80); widows: 1; background-color: rgb(255, 255, 255);"> </span><font color="#222222" style="widows: 1;">3D HISTECH .mrxs brightfield
differs substantially from fluorescence images stored in .mrxs. They are essentially two different file formats, thus doubling the work required. </font></li><li><span style="color: rgb(34, 34, 34); widows: 1; background-color: rgb(255, 255, 255);">Based on recent data submissions and information from the community, 3DHISTECH scanners default to JPEG-XR compression when acquiring fluorescence data. Another doubling
of work and complexity, as we support both compressed and uncompressed data, in brightfield and fluorescence.</span></li></ul>
<div class="adL" style="widows: 1;"><span class="im">
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">As a team we are not comfortable with releasing a reader implementation that works on a limited set of 3D HISTECH .mrxs variants</font><font color="#222222">, or
requires</font> <font color="#222222">time consuming and computationally expensive reprocessing and pyramid creation, just because of the implementation choices made in the .mrxs format. </font><font color="#222222">Also, while the software community at large
has made significant strides</font> in <font color="#222222">expanding JPEG-XR support beyond its original </font><font color="#222222">exclusive, patent-<wbr>encumbered </font><font color="#222222">Microsoft Windows implementation, a pure Java decoder remains
elusive. Work is underway to explore pure Java decoder alternatives as support for this compression type extends beyond 3D HISTECH .mrxs but it is very far from a simple addition.</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><br>
</div>
<div style="background-color: rgb(255, 255, 255);"><font>Finally, we’ll </font><font>finish with a philosophical point. The OME Consortium and the wider community has worked steadily since 2002, funded mostly by grants from non-profit charities and public
funders, to build tools for the wider scientific community. Building readers for proprietary formats has never been funded, and we don’t think it would ever be funded by any grant funding panel. New readers are created either</font> <font>by diverting our
precious resources from other projects,</font> <font>by contributions by the community (most recently by the companies themselves) or </font><font>by work commissioned by customers of Glencoe Software. We certainly listen to the community and adjust our priorities
based on requests, but we can’t do everything with limited resources. Perhaps we could crowdsource the funding for .</font>mrxs<font> but that misses the point— .mrxs is a complex, expensive, difficult, proprietary, closed format, designed to lock its users
into a single, proprietary software application. The community’s resources are finite and should be used for other things than reverse engineering this type of format— work that if subjected to peer review would be declined as a waste of community resources.
Several of those “other things” were discussed at our recent Annual Users Meeting (</font><a href="https://www.openmicroscopy.org/site/community/minutes/meetings/10th-annual-users-meeting-june-2015">Presentations</a><font> and
</font><a href="https://trello.com/b/CTG2teAV/paris-2015">Trello</a><font>) and represent key technologies that the community needs to achieve its scientific goals.</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><br>
</div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">Over the last few years, we have seen efforts by several commercial imaging companies to support open formats, provide open APIs, and to make it easier for researchers
and clinicians to work with the data acquired by their instruments. We have also received specifications and input from several imaging companies, which we have used to improve our own work and output. We applaud this trend— ultimately it means scientists,
clinicians, engineers and developers spend less time dealing with data formats and more time doing science, developing new technologies and treating patients. </font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222"><br>
</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">In the case of 3DHISTECH .mrxs, the community has the power to change the situation. You can</font> <font color="#222222">condition your purchase, continued payment
of support and maintenance fees, etc on</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><br>
</div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">— the delivery of a rational, well-designed, efficient, open format</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">— use of open compression schemes</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">— support for the community’s efforts to deliver open readers for these files</font></div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><br>
</div>
<div style="background-color: rgb(255, 255, 255); color: rgb(80, 0, 80);"><font color="#222222">You can of course also commit your own development resources to help solve this problem. </font></div>
<div style="background-color: rgb(255, 255, 255);"><font><br>
</font></div>
<div>I<font style="background-color: rgb(255, 254, 254);">’m sorry we can’t give a more positive response to your email, several others on this list, and many other private emails we’ve received. As described above, we’ve explored this format extensively,
and have already spent a few developer months on it. We’d strongly encourage a discussion between the user community and the creators of this format.</font></div>
<div><font style="background-color: rgb(255, 254, 254);"><br>
</font></div>
<div><font style="background-color: rgb(254, 253, 253);">Cheers,</font></div>
<div><font style="background-color: rgb(254, 253, 253);"><br>
</font></div>
<div><font style="background-color: rgb(253, 252, 252);">Jason</font></div>
<div><font style="background-color: rgb(253, 252, 252);"><br>
</font></div>
<div><font style="background-color: rgb(253, 252, 252);">
<div>
<div>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="color: black; font-size: 12px;">--------------------</span></p>
<div>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;">Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee </span><span style="color: black;"></span></span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="color: black; font-size: 12px;"> </span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;">Phone: +44 (0) 1382 385819 </span><span style="color: black;"></span></span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;">email: <a href="mailto:j.swedlow@dundee.ac.uk" target="_blank" style="color: rgb(149, 79, 114);"><span style="color: blue;">j.swedlow@dundee.ac.uk</span></a></span><span style="color: black;"></span></span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;"> </span><span style="color: black;"></span></span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;">Web: </span><span style="color: black;"></span><span style="color: rgb(0, 0, 0);"><a href="http://www.lifesci.dundee.ac.uk/people/jason-swedlow">http://www.lifesci.dundee.ac.uk/people/jason-swedlow</a> </span></span></p>
<p class="MsoNormal" style="color: rgb(40, 40, 40);"><span style="font-size: 12px;"><span style="color: black;">Open Microscopy Environment: <span style="color: blue;"><a href="http://openmicroscopy.org/" target="_blank" style="color: rgb(149, 79, 114);">http://openmicroscopy.org</a></span></span></span></p>
</div>
</div>
<div><br>
</div>
</div>
</font></div>
</span></div>
</div>
<div style="color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<br>
</div>
<span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of "<a href="mailto:fujisaws@mskcc.org">fujisaws@mskcc.org</a>" <<a href="mailto:fujisaws@mskcc.org">fujisaws@mskcc.org</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME Users <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 10 September 2015 14:23<br>
<span style="font-weight:bold">To: </span>OME Users <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-users] 3DHistech .mrxs files - update?<br>
</div>
<div><br>
</div>
<div 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">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Bookman Old Style";
panose-1:2 5 6 4 5 5 5 2 2 4;}
@font-face
{font-family:"\@MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-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.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Bookman Old Style","serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@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]-->
<div lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Hello -<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">I assume a lot of people have contacted you about this, but we are biting our fingers waiting for OME to support 3DHistech .mrxs files. Any update or ETA?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Sho Fujisawa<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Sr. Digital Microscopist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Molecular Cytology Core Facility<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Memorial Sloan-Kettering Cancer Center<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">417 E. 68th St.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">Zuckerman Room 1834<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">New York NY 10065<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">(212) 639-6667<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: 'Bookman Old Style', serif;">(646) 888-2186<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p>=====================================================================<br>
<br>
Please note that this e-mail and any files transmitted from<br>
Memorial Sloan Kettering Cancer Center may be privileged, confidential,<br>
and protected from disclosure under applicable law. If the reader of<br>
this message is not the intended recipient, or an employee or agent<br>
responsible for delivering this message to the intended recipient,<br>
you are hereby notified that any reading, dissemination, distribution,<br>
copying, or other use of this communication or any of its attachments<br>
is strictly prohibited. If you have received this communication in<br>
error, please notify the sender immediately by replying to this message<br>
and deleting this message, any attachments, and all copies and backups<br>
from your computer.<br>
</p>
</div>
</div>
</span><br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>