<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:x="urn:schemas-microsoft-com:office:excel" 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=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle18
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
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-GB" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">Just to add that these are IMS files and that we have “patched” FIJI with the latest netCDF file with the jar from here:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp">https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">James<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><b><span style="color:#1C2674;mso-fareast-language:EN-GB">James Wainwright<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1C2674;mso-fareast-language:EN-GB">Global Applications Specialist - Microscopy Systems<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674;mso-fareast-language:EN-GB">Tel:
</span></b><span style="color:#1C2674;mso-fareast-language:EN-GB">+44 (0) 2890 237 126 ext. 2130<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674;mso-fareast-language:EN-GB">Skype:
</span></b><span style="color:#1C2674;mso-fareast-language:EN-GB">andor.j.wainwright
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674;mso-fareast-language:EN-GB">Mob:
</span></b><span style="color:#1C2674;mso-fareast-language:EN-GB">+44 (0) 7834 710 834<br>
<b>Web:</b> <a href="https://www.andor.com/microscopy-systems"><span style="color:blue">https://www.andor.com/microscopy-systems</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-GB"><br>
</span><span style="font-family:"Times New Roman",serif;color:#1F497D;mso-fareast-language:EN-GB"><img border="0" width="128" height="38" style="width:1.3333in;height:.3958in" id="Picture_x0020_1" src="cid:image002.jpg@01D42297.F0671300" alt="logo"></span><span style="mso-fareast-language:EN-GB"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-GB"> row_microscopy_support
<br>
<b>Sent:</b> 23 July 2018 15:05<br>
<b>To:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Cc:</b> row_microscopy_support <row_microscopy_support@andor.com>; WILDE Geraint <g.wilde@andor.com>; WAINWRIGHT James <J.Wainwright@andor.com><br>
<b>Subject:</b> Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We have a customer in Australia that is acquiring large Multi-point datasets. Can be upwards of 500GB data sets each time.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">They capture full Frame, no Binning (1024x1024 pixels), dual channel ( 2 simultaneous cameras acquiring) and 60-100 Z planes on multiple X/Y positions in an overnight (timelapse) protocol. These files can be upwards of 80Gb per XY position.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The problem they have is when they try and import these large data sets to FIJI it fails, however if they perform a similar experiment, only smaller in size there is no issue.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">After asking the customer to perform a couple of tests for us, this is what they discovered:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">“<b><i>Definitely looks to be a file size issue. Tried the smaller 1.5Gb files yesterday and it worked fine. Did a longer experiment (same experimental setup just with more z-slices and more time points so the file was around 60Gb and
these are failing. The only other difference was that the small files that worked had been captured using two channel sequential while the large files that don’t work were captured with dual channel simultaneous capture.”<o:p></o:p></i></b></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any advice/workaround you can supply for handling these larger datasets would be appreciated.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="mso-fareast-language:EN-GB">Phil Mullan</span></b><span style="mso-fareast-language:EN-GB"><br>
Product Support Engineer (Microscopy Systems)<br>
Europe, Middle East & Africa<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="mso-fareast-language:EN-GB">Tel: </span></b><span style="mso-fareast-language:EN-GB">+44 (0) 28 9023 7126
<b>Ext. </b>2732<br>
<b>Fax: </b>+44 (0) 28 9031 0792 <br>
<b>Web:</b> <a href="http://www.andor.com/" target="_blank"><span style="color:blue">andor.com/support</span></a>
<br>
<br>
<img border="0" width="85" height="25" style="width:.8854in;height:.2604in" id="x_Picture_x0020_1" src="cid:image003.jpg@01D42297.F0671300" alt="logo"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
___________________________________________________________________________<br>
This e-mail is confidential and is for the addressee only. Please refer to <br>
<a href="http://www.oxinst.com/email-statement">www.oxinst.com/email-statement</a> for regulatory information.
</body>
</html>