<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi James,
<div class=""><br class="">
</div>
<div class="">Thank you for submitting the sample QA files for this issue. I was able to test and reproduce the problems you described when importing through Fiji.</div>
<div class="">For further investigation into this I have added the details of these bugs to a card on the Bio-Formats 5.3 Trello board and a Trac ticket which you will be cc’d on <a href="http://trac.openmicroscopy.org/ome/ticket/13319#ticket" class="">http://trac.openmicroscopy.org/ome/ticket/13319#ticket</a>.</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 2 Feb 2017, at 15:22, James Wainwright <<a href="mailto:jimboesq@gmail.com" class="">jimboesq@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi there,
<div class=""><br class="">
</div>
<div class="">I'm having some problems opening Imaris IMS files in FIJI.</div>
<div class=""><br class="">
</div>
<div class="">I believe there is a partial workaround involving replacing the NetCDF jar with the latest one available here:</div>
<div class=""><br class="">
</div>
<div class=""><a href="http://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp" class="">http://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">This helps significantly, but there are still problems.</div>
<div class=""><br class="">
</div>
<div class="">Having done some testing, I can confirm at least the following issues:</div>
<div class=""><br class="">
</div>
<div class="">1) Time series data - there seems to be a frame limit around 7080 time points. Less than this will open, but more than this will not open with an error message. I have uploaded examples files using the QA system:</div>
<div class=""><br class="">
</div>
<div class="">2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol = 7075 frames (opens OK)<br class="">
</div>
<div class="">2016-12-14_09.26.04_Sample Prefix_WAINWRIGHT James_Protocol = 7081 frames (does not open)<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">2) 3D data - as you probably know, Imaris stores a number of different resolution volumes inside each IMS file. The problem seems to be that FIJI cannot open the largest of these. It offers only the smaller resolution. I have uploaded an example
of this using the QA system:</div>
<div class=""><br class="">
</div>
<div class="">2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol = 1024 x 1024 x 47 planes. FIJI seems to only offer the 512 and 256 pixel volumes.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Please let me know if there is anything else I can provide to try and help you resolve these issues? (No pun intended!).</div>
<div class=""><br class="">
</div>
<div class="">Many thanks</div>
<div class=""><br class="">
</div>
<div class="">James</div>
</div>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>