[ome-users] dm4 format

[Sebastien Besson (Staff)]

Hi Greg,

thanks for the offer and no rush as we not actively planning any work on this format.
If you have easy access to these special image types, feel free to upload them at
http://qa.openmicroscopy.org.uk/qa/upload/ and we will record a card/ticket to
investigate the differences between Bio-Formats and the plugin on our side.

Best,
Sebastien

On 3 Apr 2017, at 18:27, Morgan, David Gene <dagmorga at indiana.edu<mailto:dagmorga at indiana.edu>> wrote:

Sebastien,

   If it would be helpful, I can probably supply a series of dm3/dm4 files that are likely to qualify as "special image types."

--
           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<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: Monday, April 3, 2017 5:15 AM
To: users OME
Subject: Re: [ome-users] dm4 format

Hi Greg,

thanks for your answer and the additional precisions on the original DM3_Reader plugin.

We have not received any community request related to the special handling of some DM3 image
types. Let us know if you have any sample files reflecting this behavior. In the meantime, the
existence of both plugins should allow users to choose their implementation when opening DM3
files.

Best,
Sebastien

On 30 Mar 2017, at 14:26, Dr Gregory Jefferis <jefferis at mrc-lmb.cam.ac.uk<mailto:jefferis at mrc-lmb.cam.ac.uk>> wrote:

A brief comment on this thread seems in order since I am the original author of both the DM3_Reader plugin and HandleExtraFileTypes!

On 29 Mar 2017, at 17:43, Morgan, David Gene wrote:

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 canonical source for the standalone DM3 reader distributed with Fiji is here:

https://github.com/fiji/IO/blob/master/src/main/java/sc/fiji/io/DM3_Reader.java

I have not received any bug reports for a while, so it has not been updated since 22 Feb 2013. I believe this plugin may have slightly different support for a few unusual DM3 image types (e.g. EELS spectra?) compared with the bioformats reader. As mentioned earlier it does not support the DM4 format – and it is rather unlikely that I will spend time to support this given the existence of bioformats.

Best wishes,

Greg.

--
Gregory Jefferis, PhD                   Tel: +44 1223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/departments/connectomics
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