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<p>Sebastien,</p>
<p><br>
</p>
<p> Thanks for the help and information. Maybe I am just being an idiot, but this is what I see happen:</p>
<p><br>
</p>
<p> If I just try to "open" an dm4 file (from the File dropdown menu), I get a Bio-Formats import GUI. If I simply click "OK," an image window opens but it is totally white. This happens both when I check the autoscale box in the Bio-Formats dialog box
and when I don't. If I open the "brightness/contrast" tool and click "auto", I can get the image to display properly. This would work, except that I need to be able to do this in a batch process and I don't see how to incorporate the click of "OK" in the
initial Bio-Formats dialog (and the macro recorder just gives me an open command). So it opens the file, but doesn't solve my actual problem.<br>
</p>
<p><br>
</p>
<p> When I do the above using a dm3 file, it simply opens and displays properly.</p>
<p><br>
</p>
<p> After I installed DM3_Reader.class, I can use it directly from the plugins menu, and dm3 files open fine. However, when I try to open a dm4 file, I get a java.ioException error that reads "This does not seem to be a DM3 file."</p>
<p><br>
</p>
<p> I have repeated this on a Windows 7 system, a linux box and using both straight imageJ and fiji.</p>
<p><br>
</p>
<p> I will upload one of the images as you suggest.<br>
</p>
<p><br>
</p>
<p> Also, you may know about this, but there is a description of dm4 files at the bottom of this page:</p>
<p><br>
</p>
<p> <a href="http://www.er-c.org/cbb/info/dmformat/">http://www.er-c.org/cbb/info/dmformat/</a><br>
</p>
<p><br>
</p>
<p>Again, thanks for the help.<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> Tuesday, March 28, 2017 5:40 AM<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] dm4 format</font>
<div> </div>
</div>
<div>
<div>
<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><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><br class="">
</div>
<div>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><br class="">
</div>
The dm4 format is already supported in Bio-Formats via the same reader as the one used for</div>
<div>the dm3 format [1].</div>
<div><br class="">
</div>
<div>We know this support is only partial and we have already some open tickets for this format [2]. As</div>
<div>mentioned in a previous thread [3], one of our issue is the lack of proper official specification. Would</div>
<div>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><br class="">
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br class="">
</div>
<div>[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>[2] <a href="https://trac.openmicroscopy.org/ome/ticket/13057" class="">https://trac.openmicroscopy.org/ome/ticket/13057</a> </div>
<div>[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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http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
</div>
<br class="">
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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