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<p>Curtis and Sebastien,</p>
<p><br>
</p>
<p> Thanks for the explanations and for all your help. Your efforts are definitely appreciated. Keep up the good work!<br>
</p>
<p><br>
</p>
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<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
-- <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 style="color: rgb(33, 33, 33);">
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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 Curtis Rueden <ctrueden@wisc.edu><br>
<b>Sent:</b> Wednesday, March 29, 2017 10:39 AM<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] dm4 format</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi David,
<div><br>
</div>
<div>
<div>> At least to me, this seems like the dm4 file is not being recognized</div>
<div>> as an "understood format" in the same way that dm3 files are being</div>
<div>> recognized.</div>
</div>
<div><br>
</div>
<div>This is a fundamental limitation of ImageJ 1.x: file types beyond those built into ImageJ itself are handled by a special plugin called HandleExtraFileTypes. The version of HandleExtraFileTypes which ships with Fiji tries a series of different plugins,
including the DM3_Reader, and finally if nothing else works then Bio-Formats is tried.</div>
<div><br>
</div>
<div><a href="https://github.com/fiji/IO/blob/IO_-3.0.1/src/main/java/HandleExtraFileTypes.java#L141-L149" target="_blank">https://github.com/fiji/IO/<wbr>blob/IO_-3.0.1/src/main/java/<wbr>HandleExtraFileTypes.java#<wbr>L141-L149</a><br>
</div>
<div><a href="https://github.com/fiji/IO/blob/IO_-3.0.1/src/main/java/HandleExtraFileTypes.java#L493-L514" target="_blank">https://github.com/fiji/IO/<wbr>blob/IO_-3.0.1/src/main/java/<wbr>HandleExtraFileTypes.java#<wbr>L493-L514</a><br>
</div>
<div><br>
</div>
<div>You can avoid this behavior in a couple of different ways:</div>
<div><br>
</div>
<div>* Use File > Import > Bio-Formats to call Bio-Formats directly, instead of using File > Open.</div>
<div>* Use Plugins > Bio-Formats > Bio-Formats Plugins Shortcut Window, and drag-and-drop your DM4 file onto the Bio-Formats window.</div>
<div>* In Edit > Options > ImageJ2..., check the "Use SCIFIO when opening files (BETA!)" option. Then File > Open will work differently, and should invoke Bio-Formats before trying the old DM3_Reader plugin.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
<div class="gmail_extra"><br clear="all">
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<div class="m_-7824143810681232483gmail_signature">
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<div><span style="font-size:12.8px">--</span></div>
<div><span style="font-size:12.8px">Curtis Rueden</span><br>
</div>
<div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">
https://loci.wisc.edu/software</a></span></div>
<div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:<wbr>Rueden</a></span></div>
<div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">
http://forum.imagej.net/</a></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
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<br>
<div class="gmail_quote">On Wed, Mar 29, 2017 at 9:02 AM, Morgan, David Gene <span dir="ltr">
<<a href="mailto:dagmorga@indiana.edu" target="_blank">dagmorga@indiana.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr" style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
<span>
<p><br>
</p>
<div id="m_-7824143810681232483m_8556662583867326225Signature">
<div name="divtagdefaultwrapper">-- <br>
<div name="divtagdefaultwrapper"> David Gene Morgan<br>
Electron Microscopy Center<br>
047D Simon Hall<br>
IU Bloomington<br>
<a href="tel:(812)%20856-1457" value="+18128561457" target="_blank">812 856 1457</a> (office)<br>
<a href="tel:(812)%20856-3221" value="+18128563221" target="_blank">812 856 3221</a> (3200)<br>
<a href="http://iubemcenter.indiana.edu" target="_blank">http://iubemcenter.indiana.edu</a></div>
</div>
</div>
</span>
<div style="word-wrap:break-word">
<hr style="display:inline-block; width:98%">
<div id="m_-7824143810681232483m_8556662583867326225divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><span><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openm<wbr>icroscopy.org.uk</a>>
on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>><br>
</span><b>Sent:</b> Wednesday, March 29, 2017 7:08 AM
<div>
<div class="m_-7824143810681232483h5"><br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] dm4 format</div>
</div>
</font>
<div> </div>
</div>
<div>
<div class="m_-7824143810681232483h5">
<div>Hi David,
<div><br>
</div>
<div>thanks for the heads up and the additional references.</div>
<div><br>
</div>
<div>With regard to the DM3_Reader, are you referring to this plugin available from</div>
<div>the ImageJ website [1]? If so, this plugin is managed completely separately from</div>
<div>Bio-Formats and we do not know if it is actively maintained.</div>
<div><br>
</div>
<div>The DM3/DM4 reader maintained by Bio-Formats is bundled as part of the JARs</div>
<div>that are either downloaded from the OME website or shipped to the Java-8 update for</div>
<div>Fiji distributions. There should be no additional requirement in order to open dm3/dm4</div>
<div>files.</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>[1] <a href="https://imagej.nih.gov/ij/plugins/DM3_Reader.html" target="_blank">https://imagej.nih.gov/ij/<wbr>plugins/DM3_Reader.html</a> </div>
<div><br>
<div>
<blockquote type="cite">
<div>On 29 Mar 2017, at 00:45, Morgan, David Gene <<a href="mailto:dagmorga@indiana.edu" target="_blank">dagmorga@indiana.edu</a>> wrote:</div>
<br class="m_-7824143810681232483m_8556662583867326225Apple-interchange-newline">
<div>
<div dir="ltr" style="font-size:12pt; background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Sebastien,</p>
<p><br>
</p>
<p> 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" target="_blank">openmicroscopy.org</a> site, and maybe it will help you figure out the problem.
<br>
</p>
<p><br>
</p>
<div id="m_-7824143810681232483m_8556662583867326225Signature">
<div name="divtagdefaultwrapper">-- <br>
<div name="divtagdefaultwrapper"> David Gene Morgan<br>
Electron Microscopy Center<br>
047D Simon Hall<br>
IU Bloomington<br>
<a href="tel:(812)%20856-1457" value="+18128561457" target="_blank">812 856 1457</a> (office)<br>
<a href="tel:(812)%20856-3221" value="+18128563221" target="_blank">812 856 3221</a> (3200)<br>
<a href="http://iubemcenter.indiana.edu" id="m_-7824143810681232483m_8556662583867326225NoLP" target="_blank">
http://iubemcenter.indiana.edu</a></div>
</div>
</div>
<div style="word-wrap:break-word">
<hr style="display:inline-block; width:98%">
<div id="m_-7824143810681232483m_8556662583867326225divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif"><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openm<wbr>icroscopy.org.uk</a>>
on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>><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">
<div><br>
On 27 Mar 2017, at 18:23, Morgan, David Gene <<a href="mailto:dagmorga@INDIANA.EDU" target="_blank">dagmorga@INDIANA.EDU</a>> wrote:</div>
<br class="m_-7824143810681232483m_8556662583867326225Apple-interchange-newline">
<div>Hi,<br>
</div>
</blockquote>
<br>
Hi David,</div>
<div><br>
<blockquote type="cite">
<div> 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>
</div>
</blockquote>
<div><br>
</div>
<div>Thanks for contacting us, using this list to reach the Bio-Formats developers is completely fine.</div>
<br>
<blockquote type="cite">
<div> 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>
</div>
</blockquote>
<div><br>
</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>
</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/?" target="_blank">http://qa.openmicroscopy.or<wbr>g.uk/qa/upload/?</a></div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>[1] <a href="https://www.openmicroscopy.org/site/support/bio-formats5.4/formats/gatan-digital-micrograph.html" target="_blank">https://www.openmicroscopy<wbr>.org/site/support/bio-<wbr>formats5.4/formats/gatan-<wbr>digital-micrograph.html</a> </div>
<div>[2] <a href="https://trac.openmicroscopy.org/ome/ticket/13057" target="_blank">https://trac.openmicroscop<wbr>y.org/ome/ticket/13057</a> </div>
<div>[3] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-February/003881.html" target="_blank">http://lists.openmicroscop<wbr>y.org.uk/pipermail/ome-devel/<wbr>2017-February/003881.html</a> <br>
<br>
<blockquote type="cite">
<div>--<br>
David Gene Morgan<br>
Electron Microscopy Center<br>
047D Simon Hall<br>
IU Bloomington<br>
<a href="tel:(812)%20856-1457" value="+18128561457" target="_blank">812 856 1457</a> (office)<br>
<a href="tel:(812)%20856-3221" value="+18128563221" target="_blank">812 856 3221</a> (3200)<br>
<a href="http://iubemcenter.indiana.edu/" target="_blank">http://iubemcenter.indian<wbr>a.edu</a><br>
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