Get pixel witdth and hight

[Peregalli]

Hi!

I am using Fast library in python, and importing a WSI with TIFFImagePyramidImporter function and after that I am extracting some images with getPatchAsImage, with level 0 (40x magnification) and 1024x1024 image size. I want to see size of some structures, how can I get the pixel witdth and hight in micrometers or milimeters?

[smistad]

Hi

If that information is stored in your TIFF you can get that information with the getSpacing() method.

For an extracted patch at level, x, y with a specific width and height:

access = imagePyramid.getAccess(fast.ACCESS_READ)
image = access.getPatchAsImage(level, x, y, width, height)
spacing_x = image.getSpacing()[0,0]
spacing_y = image.getSpacing()[1,0]

This corresponds to the spacing for the given level of the patch.

You can also get the spacing for level 0 directly from the image pyramid:

spacing_x = imagePyramid.getSpacing()[0,0]
spacing_y = imagePyramid.getSpacing()[1,0]

[Peregalli]

Thanks for your answer! In my case those commands didnt work, but I was able to extract that information from WSI metadata.

[andreped]

I was able to extract that information from WSI metadata.

@Peregalli Would be great if you could share exactly what you did (minimalistic code example), such that we and others who might run into the same issue, may find a solution for it by finding this discussion thread :)

[smistad]

The first example I wrote was incorrect. I updated my answer.