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Images from LIF file display wrong channel

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Images from LIF file display wrong channel

Postby albot » Wed Jun 20, 2012 9:59 am

Hi all,

One of our users has discovered that there seems to be an issue with the import of her lif files.

She has one file which is composed of many confocal images acquired with 2 channels Alexa 555 and Alexa 657.
When importing into OMERO, most of the images display the right channels, apart from 4 where it showed Alexa 647 for both channels.

Is there a chance that it might have been fixed in OMERO 4.4 ?
The file would be available on a dropbox if you need access to it. We could also provide you with the names of the respective files.

Best,
Alexander

OMERO 4.3.4 server with OMERO 4.3.3 client
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Re: Images from LIF file display wrong channel

Postby mlinkert » Mon Jun 25, 2012 8:55 pm

Hi Alexander,


One of our users has discovered that there seems to be an issue with the import of her lif files.

She has one file which is composed of many confocal images acquired with 2 channels Alexa 555 and Alexa 657.
When importing into OMERO, most of the images display the right channels, apart from 4 where it showed Alexa 647 for both channels.

Is there a chance that it might have been fixed in OMERO 4.4 ?


I believe that this has already been fixed, but we can certainly double-check if you are able to provide one of the files. If you need a place to upload the file, please let me know and I will send instructions privately.

Regards,
-Melissa
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Re: Images from LIF file display wrong channel

Postby albot » Tue Jun 26, 2012 11:33 am

Hi Melissa,

If you don't mind could you send me the instructions for how to provide the files?

Some of our users use those type of image files (LIFs) and would like to upload them to our OMERO system.

Thanks a lot.

Best regards,
Alexander
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Posts: 49
Joined: Wed Jun 29, 2011 3:31 pm

Re: Images from LIF file display wrong channel

Postby mlinkert » Tue Jun 26, 2012 12:38 pm

If you don't mind could you send me the instructions for how to provide the files?


Instructions have been sent in a private message.
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Re: Images from LIF file display wrong channel

Postby albot » Tue Jun 26, 2012 1:06 pm

Thanks, Melissa.

The file has been transferred to the ftp server.

Best regards,
Alexander
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Re: Images from LIF file display wrong channel

Postby mlinkert » Thu Jun 28, 2012 3:01 pm

Hi Alexander,

The file has been transferred to the ftp server.


Fantastic, thank you.

We have just now fixed the problem, as noted here:

http://trac.openmicroscopy.org.uk/ome/ticket/9243

...so the upcoming 4.4 release of Bio-Formats/OMERO should import these files correctly.

Regards,
-Melissa
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