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<p>Sebastien,</p>
<p><br>
</p>
<p> You are correct and it was my mistake that took me to the DM3_reader on the ImageJ website. It definitely does _not_ read dm4 files. Without including it, I can read a dm3 file "effortlessly" but doing the same thing with a dm4 file takes me to the
Bio-Formats import page instead of simply opening the file. Once I tell the importer what I want to do, the dm4 file opens fine. At least to me, this seems like the dm4 file is not being recognized as an "understood format" in the same way that dm3 files
are being recognized.<br>
</p>
<p><br>
</p>
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-- <br>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
David Gene Morgan<br>
Electron Microscopy Center<br>
047D Simon Hall<br>
IU Bloomington<br>
812 856 1457 (office)<br>
812 856 3221 (3200)<br>
http://iubemcenter.indiana.edu</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Sebastien Besson (Staff) <s.besson@dundee.ac.uk><br>
<b>Sent:</b> Wednesday, March 29, 2017 7:08 AM<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] dm4 format</font>
<div> </div>
</div>
<div>Hi David,
<div class=""><br class="">
</div>
<div class="">thanks for the heads up and the additional references.</div>
<div class=""><br class="">
</div>
<div class="">With regard to the DM3_Reader, are you referring to this plugin available from</div>
<div class="">the ImageJ website [1]? If so, this plugin is managed completely separately from</div>
<div class="">Bio-Formats and we do not know if it is actively maintained.</div>
<div class=""><br class="">
</div>
<div class="">The DM3/DM4 reader maintained by Bio-Formats is bundled as part of the JARs</div>
<div class="">that are either downloaded from the OME website or shipped to the Java-8 update for</div>
<div class="">Fiji distributions. There should be no additional requirement in order to open dm3/dm4</div>
<div class="">files.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://imagej.nih.gov/ij/plugins/DM3_Reader.html" class="">https://imagej.nih.gov/ij/plugins/DM3_Reader.html</a> </div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 29 Mar 2017, at 00:45, Morgan, David Gene <<a href="mailto:dagmorga@indiana.edu" class="">dagmorga@indiana.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<p class="">Sebastien,</p>
<p class=""><br class="">
</p>
<p class=""> I think I have solved my own problem with a bit of fooling around and finesse, but the DM3_Reader still seems unable to open any of the dm4 files I have. I did upload one to the
<a href="http://openmicroscopy.org" class="">openmicroscopy.org</a> site, and maybe it will help you figure out the problem.
<br class="">
</p>
<p class=""><br class="">
</p>
<div id="Signature" class="">
<div name="divtagdefaultwrapper" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
-- <br class="">
<div name="divtagdefaultwrapper" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
David Gene Morgan<br class="">
Electron Microscopy Center<br class="">
047D Simon Hall<br class="">
IU Bloomington<br class="">
812 856 1457 (office)<br class="">
812 856 3221 (3200)<br class="">
<a href="http://iubemcenter.indiana.edu" class="" id="NoLP">http://iubemcenter.indiana.edu</a></div>
</div>
</div>
<div class="" style="word-wrap:break-word">
<hr tabindex="-1" class="" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><b class="">From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Sent:</b> Tuesday, March 28, 2017 5:40 AM<br class="">
<b class="">To:</b> users OME<br class="">
<b class="">Subject:</b> Re: [ome-users] dm4 format</font>
<div class=""> </div>
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class=""><br class="">
On 27 Mar 2017, at 18:23, Morgan, David Gene <<a href="mailto:dagmorga@INDIANA.EDU" class="">dagmorga@INDIANA.EDU</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi,<br class="">
</div>
</blockquote>
<br class="">
Hi David,</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class=""> This question is really for the developers of Bio-Formats, but this seems to be the best way to send the question to them... I apologize for bugging everyone else!<br class="">
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Thanks for contacting us, using this list to reach the Bio-Formats developers is completely fine.</div>
<br class="">
<blockquote type="cite" class="">
<div class=""> Is there a plan to include Gatan's DigitalMicrograph dm4 format in the future. Both imageJ and FIJI read the previous version (dm3) without any trouble, but neither appears to understand the dm4 format. I'm sure others would find it useful
to be able to read such files. The format appears to be a wrinkle on the dm3 format, and there are descriptions available on the web. Thanks.<br class="">
</div>
</blockquote>
<div class=""><br class="">
</div>
The dm4 format is already supported in Bio-Formats via the same reader as the one used for</div>
<div class="">the dm3 format [1].</div>
<div class=""><br class="">
</div>
<div class="">We know this support is only partial and we have already some open tickets for this format [2]. As</div>
<div class="">mentioned in a previous thread [3], one of our issue is the lack of proper official specification. Would</div>
<div class="">you be able to upload one of your failing dm4 files to <a href="http://qa.openmicroscopy.org.uk/qa/upload/?" class="">http://qa.openmicroscopy.org.uk/qa/upload/?</a></div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://www.openmicroscopy.org/site/support/bio-formats5.4/formats/gatan-digital-micrograph.html" class="">https://www.openmicroscopy.org/site/support/bio-formats5.4/formats/gatan-digital-micrograph.html</a> </div>
<div class="">[2] <a href="https://trac.openmicroscopy.org/ome/ticket/13057" class="">https://trac.openmicroscopy.org/ome/ticket/13057</a> </div>
<div class="">[3] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-February/003881.html" class="">http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-February/003881.html</a> <br class="">
<br class="">
<blockquote type="cite" class="">
<div class="">--<br class="">
David Gene Morgan<br class="">
Electron Microscopy Center<br class="">
047D Simon Hall<br class="">
IU Bloomington<br class="">
812 856 1457 (office)<br class="">
812 856 3221 (3200)<br class="">
<a href="http://iubemcenter.indiana.edu/" class="">http://iubemcenter.indiana.edu</a><br class="">
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