Extracting Whole Slide Image by Using OpenslideAPI

TAE WOOK OH taewooko at gmail.com
Tue Nov 22 15:06:31 EST 2011

Hi openslide folks,

I have a question for extracting Whole Slide Image by Using OpenslideAPI.

I called below function to extract image from whole slide image.  (.svs)

openslide_read_region(osr, buf, startCoordinateX, endCoordinateY, 0,
tile_w, tile_h);

For testing,

I execute command like as follows.

command: (region5 is the command that I modified ... it's exactly same as
openslideTiler with different argument order.

region inputFileName startCoordinateX startCoordinateY endCoordinateX

Actual command:
region5 TCGA-08-0352-01Z-00-DX2.svs 0 12425 500 12925

Input image : TCGA-08-0352-01Z-00-DX2.svs

As a result,
ppm file was generated

When I checked the starting coordinate (0, 12425) in the whole slide image
by using aperio,
the coordinate seems different like (0, 13017) ...

I think that there is coordinate difference bug.

For example, based on theory, If i want to extract point (X, Y) from the
whole slide image,
I need to extract the coordinate (X - (width/2), Y-(height/2)).

Starting point( 2000, 2000), extracting image width (500), extracting image
height (500)

then, the starting point X, Y should be 2000 - (500 / 2) = 1750

X, Y( 1750, 1750)

However, according to the testing, I need to set up extracting starting
coordinate (X- (width/2)), Y- (height/2) - height).

I seem like I need to decrease coordinate height again.

X = 2000 - (500/2) = 1750
Y = 2000 - (500/2) - 500 = 1250

X, Y (1750, 1250)

Is this openslideAPI bug ? I am thinking that I can manually change the
coordinate in the worst case..

But, if somebody know the solution, it would be great help for me.

Thanks in advance.


Tae Wook (Steve) Oh

Intern for advanced biomedical database
Research & development
Center for Comprehensive Informatics
Emory University

Email: TOH3 at emory.edu, taewooko at gmail.com
Web: student.gsu.edu/~toh2 <http://student.gsu.edu/%7Etoh2>
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