FAST-Pathology

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Converting segmentation.tiff to 'imagename'.tiff

10

This is just a query. I am running FastPAthology v1.0.1 on Win 11. I run a pipeline for all images in my project. Is there a way to name the...

ajr82

openslide is installed under anaconda on Mac

2

Hi While installing Fast-Pathogy on Mac, I encountered the error messages like below dyld[45798]: Library not loaded: /usr/local/opt/libtiff/lib/libtiff.5.dylib Referenced from: /Users/xinqi/Desktop/DigitalPathology/fastpathology_macos10.13_1.0.0/lib/libFAST.4.3.0.dylib Reason: tried: '/usr/local/opt/libtiff/lib/libtiff.5.dylib' (no such file), '/usr/local/lib/libtiff.5.dylib' (no such...

CindyQi7788

I feel like the GUI is missing a menu bar. Looks rather strange without it. Does not need to have lots of features. Perhaps being able to close the software...

andreped

I just tried running inference in batch mode using the two images in the test data using the BACH model. What happens is that a progress bar shows. All good....

andreped

Strange zoom behaviour

1

If you render a WSI and zoom as far in as you can, you will observe that you are unable to zoom out again. The rendered image just becomes black,...

andreped

Just run the nuclei segmentation pipeline which follows with FP on a local WSI, and observed that the rendered segmentations were off. This was observed for a WSI stored in...

andreped

Some issues with display of rendering, etc.

1

I have briefly tested the new FastPathology version. More stable. but some issues: 1. crashes when I try to load small tiff files, but not large ones. When I test...

SahPet

It might be a good idea to create a model zoo or pipeline hub, for storing all the pipelines we create and make openly available. That way, if people want...

andreped

Similar to https://github.com/AICAN-Research/FAST-Pathology/issues/32, if you zoom out, small objects become invisible. In that scenario it makes sense to merge all together, or similar, if they are close, when rendering are...

andreped

When rendering results, for instance for nuceli, the segmentations become quite invisible when zooming out. I think it might be a good idea to add some type of rendering effect...

andreped