<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<br>
Hi all<br>
<br>
On a related note, it seems that those new flex files are sometime
loaded incorrectly. I reported it a while back
(<a class="moz-txt-link-freetext" href="https://trac.openmicroscopy.org.uk/ome/ticket/11382">https://trac.openmicroscopy.org.uk/ome/ticket/11382</a> I think). I can
confirm the issue is still present in 5.0.<br>
<br>
<br>
Thanks <br>
Anatole<br>
<br>
<br>
<div class="moz-cite-prefix">On 19/03/2014 17:39, Balaji Ramalingam
wrote:<br>
</div>
<blockquote cite="mid:CF4F836E.B51A%25b.ramalingam@dundee.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div>Hi,</div>
<div><br>
</div>
<div>Here’s more, </div>
<div>All the API calls are documented in here,</div>
<div>Please search for getWells*/getPlate*,</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/bio-formats/5.0.0/api/ome/xml/meta/MetadataRetrieve.html">http://downloads.openmicroscopy.org/bio-formats/5.0.0/api/ome/xml/meta/MetadataRetrieve.html</a></div>
<div><br>
</div>
<div>That should give you all the options that are supported (and
the signatures as well).</div>
<div>Once we get the files, I can suggest a small code snippet to
extract the details as requested.</div>
<div><br>
</div>
<div>Best,</div>
<div>Balaji</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<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>Balaji Ramalingam
<<a moz-do-not-send="true"
href="mailto:b.ramalingam@dundee.ac.uk">b.ramalingam@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, 19
March 2014 15:24<br>
<span style="font-weight:bold">To: </span>"Bonamy, Ghislain"
<<a moz-do-not-send="true"
href="mailto:ghislain.bonamy@novartis.com">ghislain.bonamy@novartis.com</a>>,
"<a moz-do-not-send="true"
href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>"
<<a moz-do-not-send="true"
href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re:
[ome-devel] Opera Flex file lattest changes<br>
</div>
<div><br>
</div>
<div>
<div 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>Hi,</div>
<div><br>
</div>
<div>The following page lists the supported metadata fields
for the flex format,</div>
<div><a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/bio-formats4/formats/evotecperkinelmer-opera-flex-metadata.html">http://www.openmicroscopy.org/site/support/bio-formats4/formats/evotecperkinelmer-opera-flex-metadata.html</a></div>
<div><br>
</div>
<div>It would be great if you could upload a sample set
(images from one or two wells) to , </div>
<div><a moz-do-not-send="true"
href="http://qa.openmicroscopy.org.uk/qa/upload/?">http://qa.openmicroscopy.org.uk/qa/upload/?</a></div>
<div><br>
</div>
<div>This will allow us to check the files locally and
suggest suitable API calls.</div>
<div><br>
</div>
<div>Best,</div>
<div>Balaji</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<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><Bonamy>,
Ghislain <<a moz-do-not-send="true"
href="mailto:ghislain.bonamy@novartis.com">ghislain.bonamy@novartis.com</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 17
March 2014 11:27<br>
<span style="font-weight:bold">To: </span>"<a
moz-do-not-send="true"
href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>"
<<a moz-do-not-send="true"
href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-devel]
Opera Flex file lattest changes<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:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 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;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-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;}
/* List Definitions */
@list l0
{mso-list-id:1273047712;
mso-list-type:hybrid;
mso-list-template-ids:1352151110 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></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 link="blue" vlink="purple" lang="EN-US">
<div class="WordSection1">
<p class="MsoNormal">Hi everyone,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It has been a while since I
last posted. I had a quick question, which Melissa
can probably answer. The flex file form changed
slightly in v2.0 of Evoshell. In particular the
file structure. The microscope now generates the
files as 1 file per field (as opposed to one file
per image). As before the rest of the dimensions
(ie. Z-stacks and channels) are encoded into the
same file.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I was wondering how I could
request the metadata for a full well in s ingle
call? In particular I would like to make our
webservice that retrieves the images compatible
with the previous version with as little changes
as possible. If there was a way to do things like:<o:p></o:p></p>
<p class="MsoListParagraph"
style="text-indent:-.25in;mso-list:l0 level1 lfo1"><!--[if !supportLists]--><span
style="mso-list:Ignore">1)<span
style="font-style: normal; font-variant:
normal; font-weight: normal; font-size: 7pt;
line-height: normal; font-family: 'Times New
Roman';">
</span></span><!--[endif]-->Get the number of
fields for Well B01 (002001*)<o:p></o:p></p>
<p class="MsoListParagraph"
style="text-indent:-.25in;mso-list:l0 level1 lfo1"><!--[if !supportLists]--><span
style="mso-list:Ignore">2)<span
style="font-style: normal; font-variant:
normal; font-weight: normal; font-size: 7pt;
line-height: normal; font-family: 'Times New
Roman';">
</span></span><!--[endif]-->Get the image slice
for WellB01 Channel2, Z-stack <o:p>
</o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">That would be perfect.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance for the help.
Hopefully this is clear, otherwise I can post more
details.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Ghislain Bonamy, PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">__________________________________________<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Group Leader<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Novartis<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Institute for<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Tropical<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
Arial, sans-serif;">Diseases<o:p></o:p></span></p>
</div>
</div>
</div>
</span><br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span></div>
</div>
</span><br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
ome-devel mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a>
</pre>
<br>
<pre class="moz-signature" cols="72">--
Anatole Chessel, PhD
Research associate
University of Cambridge
Tennis Court Road, Cambridge CB2 1PD
tel: +44 (0)1223 334065</pre>
</blockquote>
</body>
</html>