[ome-devel] bug importing dm3 files

Will Moore will at lifesci.dundee.ac.uk
Mon Aug 1 13:28:09 BST 2011 

Hi Jacki,

Basically everything can be explained by the differences between  
Insight and Importer.....

On 1 Aug 2011, at 12:51, Jacki Goldman wrote:

> 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?

Insight tries to render the image after it's imported, to show a  
thumbnail of the new image. This causes the error that we're seeing  
(black thumbnail etc).
Importer doesn't try to render the image, so no errors (until you try  
to view in Insight).

>
> 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.
> <image003.png><image004.png>
> Imported with .tif file
>
> Imported without .tif file
>
> <image005.png><image002.png>

I think this is due to another bug in Importer http://trac.openmicroscopy.org.uk/ome/ticket/6247-
Currently, importer doesn't add the "Original Metadata" to imported  
images. If you import the DM3 alone, using Insight, you should still  
see the "Original Metadata".


   Will.


>
>
> 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.
>
>
> <image001.png>
> 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
> 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
>
>
> *******************************************
> Jacki Goldman
> Science Application Developer
> London Research Institute
> Cancer Research UK
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> email: Jacki.Goldman at cancer.org.uk
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> William Moore
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
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> Phone 01382 386364
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> We may monitor all incoming and outgoing emails in line with current  
> legislation. We have taken steps to ensure that this email and  
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> responsibility to ensure that viruses do not adversely affect you.
> Cancer Research UK
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> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street,  
> London EC1V 4AD.
>
> William Moore
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> Phone 01382 386364
> http://openmicroscopy.org
>
>
>
>
>
>
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above- 
> named person(s). If you are not the intended recipient, notify the  
> sender immediately, delete this email from your system and do not  
> disclose or use for any purpose.
>
> We may monitor all incoming and outgoing emails in line with current  
> legislation. We have taken steps to ensure that this email and  
> attachments are free from any virus, but it remains your  
> responsibility to ensure that viruses do not adversely affect you.
> Cancer Research UK
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> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street,  
> London EC1V 4AD.

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org





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