Problem accessing Leica fluorescence images
bgilbert at cs.cmu.edu
Wed Feb 4 01:31:18 EST 2015
On 02/03/2015 11:44 AM, Freed, Melanie wrote:
> I have a bunch of Leica fluorescence images. Some with 3 channels
> (red, green, blue) and others with two channels (green, blue). I'm
> trying to read them in, but get the following error when I run
> openslide_get_level_count: "Found multiple macro images".
OpenSlide currently doesn't support fluorescence images for any file
format. That will require API changes to fix.
> And when I try to read the dimensions of level 0 using
> openslide_get_level_dimensions I get a segmentation fault.
openslide_get_level_dimensions() expects pointers to int64_t values that
it can fill in, but you're passing NULL.
> Is there any workaround?
Not with OpenSlide. You could try Bio-Formats.
If you're sufficiently motivated, you can also extract the pixel data
yourself: the XML in the ImageDescription tag of the first TIFF
directory tells you which TIFF directories to read for the pixel data.
You should then be able to read the pixels through libtiff. You'll want
the <image> (or <image>s) with a <view> that doesn't match the
<collection> dimensions. For the highest-resolution level, read the
TIFF directories specified in the "ifd" attribute for the <dimension>s
which have an "r" of 0; the "c" value refers to a <channel> in
<channelSettings>. This is obviously less than ideal.
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