<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><br></div>Hi Roger,<div><br><div>each file is about 410 MB, that would last some time! I don't have access to the microscope (and the Nikon software) to produce a smaller one.</div><div><br></div><div>Regards</div><div>Karsten</div><div><br><div><div>Am 15.07.2014 um 13:00 schrieb <a href="mailto:ome-users-request@lists.openmicroscopy.org.uk">ome-users-request@lists.openmicroscopy.org.uk</a>:</div><br class="Apple-interchange-newline"><blockquote type="cite">Send ome-users mailing list submissions to<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="Apple-tab-span" style="white-space:pre"> </span>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br>or, via email, send a message with subject or body 'help' to<br><span class="Apple-tab-span" style="white-space:pre"> </span>ome-users-request@lists.openmicroscopy.org.uk<br><br>You can reach the person managing the list at<br><span class="Apple-tab-span" style="white-space:pre"> </span>ome-users-owner@lists.openmicroscopy.org.uk<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of ome-users digest..."<br>Today's Topics:<br><br> 1. Re: missing images reading Nikon nd2 files (Curtis Rueden)<br> 2. Re: missing images reading Nikon nd2 files (Roger Leigh)<br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Von: </b></span><span style="font-family:'Helvetica';">Curtis Rueden <ctrueden@wisc.edu><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Betreff: </b></span><span style="font-family:'Helvetica';"><b>Aw: [ome-users] missing images reading Nikon nd2 files</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Datum: </b></span><span style="font-family:'Helvetica';">14. Juli 2014 23:06:08 MESZ<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>An: </b></span><span style="font-family:'Helvetica';">Karsten <karo13de@googlemail.com><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Kopie: </b></span><span style="font-family:'Helvetica';">OME-users mailing list <ome-users@lists.openmicroscopy.org.uk><br></span></div><br><br><div dir="ltr">Hi everyone,<div><br></div><div><div>> Importing nd2 files (two) delivers one (3-channel) image less than the</div><div>> NIS Elements Viewer.</div></div><div><br></div><div>For the archives: this report emerged from a related thread on the ImageJ mailing list, which you can find at:</div>
<div><a href="https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;cc9bcbc2.1407">https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;cc9bcbc2.1407</a><br></div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Mon, Jul 14, 2014 at 3:25 PM, Karsten <span dir="ltr"><<a href="mailto:karo13de@googlemail.com" target="_blank">karo13de@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Importing nd2 files (two) delivers one (3-channel) image less than the NIS Elements Viewer.<br>
<br>
This happens under ImageJ, Fiji and the commandline tool showinf.<br>
<br>
The meta data show the reduced number of images, still the list of the scanning table coordinates show the full number of images extended by a constant dummy coordinate to the number of (1-channel) images found from bioformats software.<br>
<br>
I attache the output of showinf.<br>
<br>
The second file delivers also one image less than the Nikon Viewer. Additionally the metadata show a different structure by dividing the list of images in a large number of series. According the microscope users, they did not change anything saving the second data file.<br>
<br>
One image less is possibly not so important. However for the sake of correctness it could be improved.<br>
<br>
Thanks in advance for any help<br>
<span class="HOEnZb"><font color="#888888"><br>
Karsten<br>
<a href="mailto:karo13de@googlemail.com">karo13de@googlemail.com</a><br>
<br>
<br>
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<br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Von: </b></span><span style="font-family:'Helvetica';">Roger Leigh <rleigh@dundee.ac.uk><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Betreff: </b></span><span style="font-family:'Helvetica';"><b>Aw: [ome-users] missing images reading Nikon nd2 files</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>Datum: </b></span><span style="font-family:'Helvetica';">15. Juli 2014 11:54:54 MESZ<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(127, 127, 127, 1.0);"><b>An: </b></span><span style="font-family:'Helvetica';"><ome-users@lists.openmicroscopy.org.uk><br></span></div><br><br>On 14/07/14 21:25, Karsten wrote:<br><blockquote type="cite"><br>Importing nd2 files (two) delivers one (3-channel) image less than the NIS Elements Viewer.<br><br>This happens under ImageJ, Fiji and the commandline tool showinf.<br><br>The meta data show the reduced number of images, still the list of the scanning table coordinates show the full number of images extended by a constant dummy coordinate to the number of (1-channel) images found from bioformats software.<br><br>I attache the output of showinf.<br><br>The second file delivers also one image less than the Nikon Viewer. Additionally the metadata show a different structure by dividing the list of images in a large number of series. According the microscope users, they did not change anything saving the second data file.<br><br>One image less is possibly not so important. However for the sake of correctness it could be improved.<br><br>Thanks in advance for any help<br></blockquote><br>Dear Karsten,<br><br>Would it be possible for you to upload this image (or any sample image<br>demonstrating this problem) using<br>http://qa.openmicroscopy.org.uk/qa/upload/ so that we can investigate<br>the problem further?<br><br><br>Many thanks,<br>Roger Leigh<br><br>--<br>Dr Roger Leigh -- Open Microscopy Environment<br>Wellcome Trust Centre for Gene Regulation and Expression,<br>College of Life Sciences, University of Dundee, Dow Street,<br>Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br><br><br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br><div apple-content-edited="true">
<div>Karsten</div><div><a href="mailto:karo13de@googlemail.com">karo13de@googlemail.com</a></div><div><br></div><br class="Apple-interchange-newline">
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