[ome-users] Bio-Formats ImageJ bit depth

[Roger Leigh]

On 16/02/2013 16:24, Tom Bongiorno wrote:
> Hello, I am using the Bio-Formats plugin on ImageJ to import JPEG2000
> images.  Although all the images are 16-bit, when using the "Measure"
> command, the dynamic range of the mean pixel value seems to be variable
> (i.e. dependent on the particular image).  If I select part of my image
> and run the "Fill" command (to get a black square), the mean pixel value
> will be 0.  But when I run the "Invert" command on the filled region (to
> get a white square), the mean pixel value is inconsistent (I'd expect
> 65535).  Some values I've gotten are 1757, 2449, 6832, and 7902.
>
> Any assistance or explanation would be greatly appreciated.

Hi Tom,

This looks like it's down to the way imagej implements the "invert"
command--it's not specific to the Bio-Formats plugin.  The invert
command inverts within the range of the min/max pixel intensity of all
the pixels of your image, rather than the full 16-bit range.  In all
your examples above, the range of values you get are probably the value
of the max intensity pixel in your image.  See invert16BitStack() in
ij/plugin/filter/Filters.java.  I agree that this is not entirely intuitive!

Select all, set min/max grey level in analyze->set measurements, and
then analyze->measure to determine that, for example.

If what you want is a complete inversion of the full 16-bit range, I
suggest as a workaround that you create an image of the same size and
bit depth with all pixels set to 65535, and then use the
calculator/calculator plus to subtract your image from this one, which
should do what you want.


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