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computationalpathologygroup / ASAP

Program for the analysis and visualization of whole-slide images in digital pathology
https://computationalpathologygroup.github.io/ASAP/
GNU General Public License v2.0
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Annotation done in other zoom level is not correct #142

Closed euwern closed 5 years ago

euwern commented 5 years ago

I notice that the polygon annotation done in other zoom level (say: 9000 pixel) is not correct when viewed in (3000 pixel). See attached images.

Annotation done in (9000pixel) https://bit.ly/2UgkpVO

Annotation viewed in (3000 pixel) https://bit.ly/2Uq2VWU

GeertLitjens commented 5 years ago

Annotations are always stored with pixel coordinates at the highest resolution. You can convert resolutions by getting the requested level downsample and dividing the coordinates (getLevelDownsample member function on an image)

euwern commented 5 years ago

Annotations are always stored with pixel coordinates at the highest resolution. You can convert resolutions by getting the requested level downsample and dividing the coordinates (getLevelDownsample member function on an image)

But there is a bug in the ASAP program. Since Annotation viewed in ASAP (at 3000 pixel) is different from Annotation done (in 9000 pixel). Is this going to be fixed?

GeertLitjens commented 5 years ago

I'm sorry, I don't know what you mean exactly and the links to the images you posted don't work.

euwern commented 5 years ago

Annotation done in (9000pixel) zz

Annotation viewed in (3000 pixel) zz1

GeertLitjens commented 5 years ago

Hmm, I have not seen this before. What filetype are you using with which version of ASAP (+ operating system)

euwern commented 5 years ago
GeertLitjens commented 5 years ago

Ok, so I'm guessing this is related to an outdated version of OpenSlide. You need version 3.4.1 which is not in the standard repositories of Ubuntu 16.04, only from 17 on. So you need to install that manually, or upgrade Ubuntu. If you install it manually do not forget to remove the old 3.4.0 package

euwern commented 5 years ago

ok, the suggested solution works. Thanks.

I have another question, when I am annotating with polygon, how can I navigate my viewpoint? By switching from PolyAnnotation to Span mode I lose the annotation.

GeertLitjens commented 5 years ago

You can press the mouse wheel to pan and scroll the mouse wheel to zoom while making an annotation.