[ome-users] Bug upon import of czi files (fwd)

[Johannes Schindelin]

Sorry, reposting from the correct mail address because the mailing list is
not moderated.

---------- Forwarded message ----------
Date: Tue, 07 May 2013 08:11:47 -0500 (CDT)
From: Johannes Schindelin <schindelin at wisc.edu>
To: Thorsten Lemke <lemke at lemkesoft.de>
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Bug upon import of czi files

Hi Thorsten,

On Tue, 7 May 2013, Thorsten Lemke wrote:

> the loci_tools.jar does only produce a black image upon import of the
> attached file.
>
> Any idea?

This is not a bug in the software but in the understanding of how images
are made up. Your image is stored as an (unsigned) 16-bit image, i.e. it
pretends to have values in the range 0-65535. However, the pixel values
are in the range 0-4047, suggesting that it is actually 12-bit (range
0-4095).

You can readily see this by inspecting the histogram (which you should
almost always do, anyway, to see whether the data are saturated).

Two remedies are available: you can check the "auto-scale" checkbox, or
you can adjust brightness & contrast after loading.

Hth,
Johannes