Posted by
jchanson on
Jan 04, 2008; 9:49pm
URL: http://imagej.273.s1.nabble.com/ImageJ-driving-AVT-Guppy-CCD-cam-tp3697467p3697476.html
>Can anyone tell me if I am able to open svs file in imageJ
Yan -
I've heard from the vendor that the SVS files actually follows the
TIF file format specification. When I've tried renaming an SVS file to a
TIF file, it doesn't correctly open in ImageJ. When I try to open a
renamed SVS with Photoshop, it opens correctly. I've never quite figured
out why this is. I'm assuming that it's because they follow the TIF
standard, but they may be using it in an unconventional way that not
everyone supports.
An even bigger issue, however, is the size of the SVS files. For
my work, a typical SVS file is well over 10K x 20K (e.g., for an RGB
image, file size is >600MB). The image analysis tools within the Aperio
software get around this by analyzing chunks of a specified width & height
(e.g., 1000 x 1000 pixel "tiles").
Here are what I think you're main options are:
- You're best bet will be to export the images as TIF from ImageScope
and then open them in ImageJ.
- The next best option would be to see if someone on this list can help
decipher why the SVS file isn't opening from within ImageJ.
- A third option might be to work with Aperio to get their help creating
an "analysis algorithm" for submitting images for analysis to ImageJ.
In any of these cases, you will need to determine what the largest
file size you can pass to ImageJ and do something to make sure that you're
never passing anything larger to ImageJ (e.g., exporting specific
sub-regions or using "tiling" to limit the file sizes).
Jeff Hanson
Senior Imaging Analyst
Eli Lilly and Company
[hidden email]