[BioC] handling 12 bit tiffs in EBImage

Gregoire Pau gregoire.pau at embl.de
Fri Jun 11 22:39:51 CEST 2010

Hi Rajarshi,

In the TIFF format, 12-bit images are stored in 16-bit. EBImage supports 
these images but they have to be scaled by a factor of 16 (2^4), to 
adjust the dynamic range.

The following commands should work:
 > library(EBImage)
 > x = readImage('image.tiff')*16
 > display(x)

If the signal is too faint, images have to be rescaled before being 
displayed, e.g. using normalize(), which performs the linear scaling (x 
- min(x))/ (max(x) - min(x)).

 > display(normalize(x))

Hope this helps,
Best regards,

Gregoire Pau
EMBL Research Officer

Rajarshi Guha wrote:
> Hi, I have a collection of 12 bit tiffs that I would like to analyze
> using EBImage. However, for the images to show via display() I need to
> convert them to 8 bit (say by using convert on the command line). Is
> EBImage capable of handling these types of directly? Or do I always
> need to sale down to 8 bit outside of R?

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