[ome-users] dm4 format

[Morgan, David Gene]

Sebastien,


    Thanks for the help and information.  Maybe I am just being an idiot, but this is what I see happen:


    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.


    When I do the above using a dm3 file, it simply opens and displays properly.


     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."


    I have repeated this on a Windows 7 system, a linux box and using both straight imageJ and fiji.


    I will upload one of the images as you suggest.


    Also, you may know about this, but there is a description of dm4 files at the bottom of this page:


            http://www.er-c.org/cbb/info/dmformat/


Again, thanks for the help.


--
            David Gene Morgan
        Electron Microscopy Center
             047D Simon Hall
             IU Bloomington
          812 856 1457 (office)
          812 856 3221 (3200)
      http://iubemcenter.indiana.edu
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk>
Sent: Tuesday, March 28, 2017 5:40 AM
To: users OME
Subject: Re: [ome-users] dm4 format


On 27 Mar 2017, at 18:23, Morgan, David Gene <dagmorga at INDIANA.EDU<mailto:dagmorga at INDIANA.EDU>> wrote:

Hi,

Hi David,

   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!

Thanks for contacting us, using this list to reach the Bio-Formats developers is completely fine.

   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.

The dm4 format is already supported in Bio-Formats via the same reader as the one used for
the dm3 format [1].

We know this support is only partial and we have already some open tickets for this format [2]. As
mentioned in a previous thread [3], one of our issue is the lack of proper official specification. Would
you be able to upload one of your failing dm4 files to http://qa.openmicroscopy.org.uk/qa/upload/?

Best,
Sebastien

[1] https://www.openmicroscopy.org/site/support/bio-formats5.4/formats/gatan-digital-micrograph.html
[2] https://trac.openmicroscopy.org/ome/ticket/13057
[3] http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-February/003881.html

--
           David Gene Morgan
       Electron Microscopy Center
            047D Simon Hall
            IU Bloomington
         812 856 1457 (office)
         812 856 3221 (3200)
     http://iubemcenter.indiana.edu
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