[ome-users] Problem reading some DeltaVision files

[Roger Leigh]

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.

Dear Chris,

This file is definitely a signed 16-bit integer file:

% hexdump -C 2269_37C_15_R3D_D3D.dv | head -n1
00000000  00 02 00 00 00 02 00 00  0e 00 00 00 01 00 00 00
|................|

The start of the file is 4 32-bit integers, which are here little-endian
0x0200, 0x0200, 0x000e and 0x0001 (x, y, number of planes and pixel type
which are 512, 512, 14 and 16-bit signed integer, respectively).

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).


The last message at the end of
http://imagej.1557.x6.nabble.com/convert-16-byte-signed-images-to-16-byte-unsigned-raw-data-td3701472.html
has one suggestion for converting from signed 16-bit to unsigned 16-bit.
  Since your image doesn't have any negative values in this image, it
should be safe (i.e. not changing any of the pixel values).  Given the
range, it might even make sense to convert to 8-bit if this applies to
all of your other images.


Kind 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