[ome-devel] Problem with fetching image from image server

[Ilya Goldberg]

Hi Swaroop
The Composite method always returns an 8-bit TIFF (or JPEG, or PNG)-  
regardless of the bit-depth in the original TIFF.  If you specify RGB  
channels, you get an RGB TIFF, if you specify GrayChannel, you get a  
grayscale TIFF.  But its always 8 bit per channel, because the  
purpose of this method is to produce an image for display rather than  
one preserving the numerical content of the pixels.
Is this what you want to do?
Because if you want the numerical values of the pixels, you should  
use one of the GetPixels methods.  Unfortunately, those don't produce  
TIFF files - they only give you the raw pixel data.
If you just want the original TIFF, then you can use the ReadFile  
method (with no parameters other than the FileID), and it will give  
you back your original TIFF just as it was.

If the Composite method really is what you want, the specification of  
how to map Pixels channels to display channels is done using  
RedChannel, GreenChannel, BlueChannel or GrayChannel (for a grayscale  
tiff).
Each *Channel parameter has 4 components:
the channel index (Pixels coordinate in the C dimension), black  
level, white level, and gamma
e.g. GrayChannel=0,0,255,1.0
The black level and white level refer to the input range - i.e. the  
numerical range of your pixels.  The output range is always 0-255,  
because  the output is always 8 bits per channel with this method,  
because its meant for display.  If your image was an 8-bit tiff to  
start out with, then the example above will not do any scaling  
because the specified black level and white level match the 0-255  
output range.  If it was not an 8-bit tiff to start with, some  
scaling needs to occur because only 8 bits per RGB channel (or  
grayscale) can be displayed.  You can scale from min to max, or from  
0 to 4095 (for a 12-bit CCD) or 0 to 32767 for signed 16-bit, or 0 to  
65535 for unsigned 16-bit.  But remember that the pixel values in the  
resulting TIFF will always be 0-255.  This is all because its not  
physically possible to display an image with more bit depth "as is"  
without scaling.
You can determine what input range to use by looking at pixel  
statistics which are stored in the DB (look at the outputs of the  
Stack statistics module for one of your images in the Web UI).  Some  
suggestions may be to use StackMinimum and StackMaximum for your  
black level and white level.

OME attempts to "guess" at an appropriate black-level and white-level  
setting for your images when you import them (look at the  
DisplayChannel output of the "Image import" module for one of your  
images in the Web UI).  DisplayOptions has a reference to  
DisplayChannel for each of the RGB channels to indicate the mapping  
for an RGB display.

Maybe a more detailed description of what you want to do would help  
us help you better.

-Ilya




On Mar 14, 2006, at 6:45 PM, Swaroop A. Jagadish wrote:

> Hi,
> What are the right parameters to use for the white level and black  
> level
> for each channel if I'm using the Composite method to fetch the  
> image. I
> want the image  in its original form when I uploaded it (Its not a
> Z-series image - its just a simple TIFF image). Are these values  
> stored in
> the database somewhere.
>
> I tried using GetPlaneStats method to extract the min and max for each
> channel. But that doesn't seem to be helping. Any help would be  
> greatly
> appreciated.
>
> Thanks,
> Swaroop
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