[ome-users] Leica lif file problem

[Melissa Linkert]

Hi Chris,

> I am uploading a Leica lif file through the OME qa upload page. This file
> contains 21 3-channel images that in both Leica software and Imaris show
> the maximum pixel value as 4095. Opening in Fiji and Omero, the first
> channel seems to have values up to 2^16. In Fiji, the histogram of the
> first channel looks like noise from a uniform distribution, and the
> histogram of the third channel does not match what I see in other software
> either.

Thank you for reporting this problem, and for uploading an example file.
We are reviewing a fix for this here:

https://github.com/openmicroscopy/bioformats/pull/783

I expect that the fix will be included in the next release of
Bio-Formats/OMERO.

Regards,
-Melissa

On Wed, Nov 06, 2013 at 03:28:38PM +0000, Wood, Christopher wrote:
> Hi,
> 
> I am uploading a Leica lif file through the OME qa upload page. This file
> contains 21 3-channel images that in both Leica software and Imaris show
> the maximum pixel value as 4095. Opening in Fiji and Omero, the first
> channel seems to have values up to 2^16. In Fiji, the histogram of the
> first channel looks like noise from a uniform distribution, and the
> histogram of the third channel does not match what I see in other software
> either.
> 
> Thanks
> 
> Chris
> 
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