[ome-devel] bug importing dm3 files

Mon Aug 1 12:51:57 BST 2011

HI Will,

Thanks for your reply.  That clears things up.

I used the stand-alone importer. In the first reply to my original post to ome-devel,  Jmarie said the problem was with the rendering system, rather than the importer.  When I just tried to use the importer built into Insight, the import failed.  Is there a difference between the stand- alone and integrated importer that might account for this?

The metadata is present for the dm3 files.  However, it only gets imported if the corresponding .tif file is imported at the same time. If you import dm3 files on their own, no metadata is imported.  I don't know if this is a separate issue or just an indication of the fact that despite the lack of errors/warnings, the image wasn't actually imported.
[cid:image003.png at 01CC5049.CBC6CD60][cid:image004.png at 01CC5049.CBC6CD60]
Imported with .tif file

Imported without .tif file

[cid:image005.png at 01CC5049.CBC6CD60][cid:image002.png at 01CC5048.B3EEA290]

Regards,
Jacki

From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
Sent: 01 August 2011 11:52
To: Jacki Goldman
Cc: Ome-nitpick Nitpick
Subject: Re: [ome-devel] bug importing dm3 files

Hi Jacki,

 I tried importing your files and I got an error importing the EM3005_01.dm3. The error I got was due to a very large range in pixel values - this has already been reported and the ticket is http://trac.openmicroscopy.org.uk/ome/ticket/3256

The reason why one DM3 imported and the other didn't was simply because of pixel values. I guess that different scopes / samples produces different ranges of pixel data and that conversion to tiff must re-scale the pixel values to cover a smaller range?

Not sure why you didn't see this on import. Did you use the stand-alone Importer client or Insight? I used Insight for importing.

I don't see anything particularly strange with the metadata for these files.
It seems the failed import still has it's metadata intact (see screen-shot). The corresponding tiff has much less metadata: seems a lot of this is lost in the conversion.

Until we fix the bug above, you'll need to convert to tiff, or set things up to acquire DM3s with smaller ranges.

Apologies for that,

  Will.

[cid:image001.png at 01CC5044.B7CE2380]
On 1 Aug 2011, at 10:27, Jacki Goldman wrote:

Hi Will,

I have downloaded the files:
EM3005_01.dm3 (feedback ID 3909)
EM3005_01.dm3 (feedback ID 3910)

EM2999_02_001.dm3 (feedback ID 3909) - this image is from a different microscope. The import was successful and both the thumbnail and the image can be rendered.

Thanks,
Jacki
From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
Sent: 27 July 2011 16:04
To: Jacki Goldman
Cc: ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] bug importing dm3 files

Hi,

 You can upload sample files here:
http://qa.openmicroscopy.org.uk/qa/upload/

Maybe upload a dm3 and the corresponding tiff too.
Let us know what the feedback ID is and I can check what the problem is.

 Thanks,

   Will.

On 27 Jul 2011, at 09:00, Jacki Goldman wrote:

I  have been having difficulty importing EM images using OMERO importer (Beta4.3.0.win).  The images are saved as dm3 files and can also be batch converted to TIF files.

If the import only includes dm3 files, there is no metadata, but if TIF files are imported at the same time, the metadata is there (even though the metadata for the TIF files themselves is different). In both cases, no import errors are reported but the thumbnail of an imported dm3 file is just a black rectangle and  attempting to view the image generates the following error:
<image001.png>

I was going to attach some sample images, but they are too large to get through our e-mail system. Do you have another way for me to send these?

Thanks,
Jacki

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Wellcome Trust Centre for Gene Regulation & Expression
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Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
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