[ome-users] dm4 format

Wed Mar 29 15:39:56 BST 2017

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>
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 <(812)%20856-1457> (office)
>           812 856 3221 <(812)%20856-3221> (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:* 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> 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 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 <(812)%20856-1457> (office)
>           812 856 3221 <(812)%20856-3221> (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> 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 <(812)%20856-1457> (office)
>          812 856 3221 <(812)%20856-3221> (3200)
>      http://iubemcenter.indiana.edu
> _______________________________________________
> ome-users mailing list
> 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
> 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
> 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/20170329/55e85ef6/attachment.html>