[ome-users] dm4 format

Wed Mar 29 17:43:54 BST 2017

Curtis and Sebastien,

    Thanks for the explanations and for all your help.  Your efforts are definitely appreciated.  Keep up the good work!

--
            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 Curtis Rueden <ctrueden at wisc.edu>
Sent: Wednesday, March 29, 2017 10:39 AM
To: OME User Support List
Subject: Re: [ome-users] dm4 format

Hi David,

> 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.

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.

https://github.com/fiji/IO/blob/IO_-3.0.1/src/main/java/HandleExtraFileTypes.java#L141-L149
https://github.com/fiji/IO/blob/IO_-3.0.1/src/main/java/HandleExtraFileTypes.java#L493-L514

You can avoid this behavior in a couple of different ways:

* Use File > Import > Bio-Formats to call Bio-Formats directly, instead of using File > Open.
* Use Plugins > Bio-Formats > Bio-Formats Plugins Shortcut Window, and drag-and-drop your DM4 file onto the Bio-Formats window.
* 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.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Wed, Mar 29, 2017 at 9:02 AM, Morgan, David Gene <dagmorga at indiana.edu<mailto:dagmorga at indiana.edu>> wrote:

Sebastien,

    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.

--
            David Gene Morgan
        Electron Microscopy Center
             047D Simon Hall
             IU Bloomington
          812 856 1457<tel:(812)%20856-1457> (office)
          812 856 3221<tel:(812)%20856-3221> (3200)
      http://iubemcenter.indiana.edu
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Sent: Wednesday, March 29, 2017 7:08 AM

To: users OME
Subject: Re: [ome-users] dm4 format

Hi David,

thanks for the heads up and the additional references.

With regard to the DM3_Reader, are you referring to this plugin available from
the ImageJ website [1]? If so, this plugin is managed completely separately from
Bio-Formats and we do not know if it is actively maintained.

The DM3/DM4 reader maintained by Bio-Formats is bundled as part of the JARs
that are either downloaded from the OME website or shipped to the Java-8 update for
Fiji distributions. There should be no additional requirement in order to open dm3/dm4
files.

Best,
Sebastien

[1] https://imagej.nih.gov/ij/plugins/DM3_Reader.html

On 29 Mar 2017, at 00:45, Morgan, David Gene <dagmorga at indiana.edu<mailto:dagmorga at indiana.edu>> wrote:

Sebastien,

    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 openmicroscopy.org<http://openmicroscopy.org> site, and maybe it will help you figure out the problem.

--
            David Gene Morgan
        Electron Microscopy Center
             047D Simon Hall
             IU Bloomington
          812 856 1457<tel:(812)%20856-1457> (office)
          812 856 3221<tel:(812)%20856-3221> (3200)
      http://iubemcenter.indiana.edu
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto: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<tel:(812)%20856-1457> (office)
         812 856 3221<tel:(812)%20856-3221> (3200)
     http://iubemcenter.indiana.edu<http://iubemcenter.indiana.edu/>
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170329/ca0b88a2/attachment.html>