Issue in mask writer in wholeslidedata

We are having problems in reading masks files. If we use a different library then those tif/tiff files are not getting read.The general slide reading libraries are not working.Gdal is working for some of them and can be read with gdal.Can we use gdal for the purpose?

Hi,

what kind of problem/exception? The masks are a tif-variant and can be read by asap (viewer and python api) and wholeslidedata. pyvips should work too. (openslide didn't work with them when I tried it since it expected rgbs and not 1-channel masks). We have never tried gdal.

I have been using large_image to read the TIF files. https://github.com/girder/large_image. There are a lot of packages that read these images, but feel free to try large_image. I really enjoy it.

Hi, in ASAP viewer (GUI v2.0.0 nightly on Ubuntu 20.04) we do not find the option to open the TIF annotation files created by the SegmentationWriter. Particularly, after opening the raw image in ASAP viewer, I open the tab "Annotations" and then I click on "Load" button, but the new window does not even show the TIF annotation files. On the other hand, it opens XML files as annotations correctly. 1. Is there another option to load TIF files as annotations on ASAP viewer? 2. Are XML files allowed as annotation outputs of the Leaderboard 1 algorithm? Thank you very much!

Lorenzo

Dear Lorenzo,

You can open masks in ASAP, via the 'overlay' tab (it is positioned vertically) XML files are not allowed as an output.

Best wishes, Mart