[ome-users] Problem reading some DeltaVision files

[Roger Leigh]

On 14/04/15 10:31, Roger Leigh wrote:
> On 13/04/15 16:57, Chris Fromme wrote:
>> Hello,
>>       I'm having a problem in which some DeltaVision files (for
>> example, see image "2269_37C_15_R3D.dv" uploaded to OMERO, ID 10995),
>> are read into FIJI in a way that the intensities are on a scale of
>> -32728 to 32767 (instead of 0 to 65535). This then leads to a problem
>> when trying to quantitate intensity values, for example, using
>> multi-measure through the ROI manager. This happens on both a Mac OS X
>> and Windows 8 machine. As it does not happen with all DeltaVision
>> files, it may be an issue with how DeltaVision is writing the files,
>> but I don't know why that would be.
>
> I would assume that this was an option enabled prior to acquisition or a
> result of any post-processing such as deconvolution (I'm afraid I'm not
> personally familiar with deltavision/softworx, so there may be other
> reasons I'm unaware of).

To add to this, Michael Porter also had this additional information:

   It might be an OMX image, which generates (by default) potential
   negative values on reconstruction (a post-processing step).
   There are options in SoftWorx to either save as unsigned or to cut
   off negative values (which should be background/noise, according to
   the API)

If this is the case for your images, it looks like it's just a matter of
setting these options if you want it unsigned.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096