INSTALLATION.md

CLAM Installation Guide

For instructions on installing anaconda on your machine (download the distribution that comes with python 3): https://www.anaconda.com/distribution/

After setting up anaconda, first install openslide:

sudo apt-get install openslide-tools

Next, use the environment configuration file located in docs/clam.yaml to create a conda environment:

conda env create -n clam -f docs/clam.yaml

Activate the environment:

conda activate clam

Once inside the created environment, to install smooth-topk (first cd to a location that is outside the project folder and is suitable for cloning new git repositories):

git clone https://github.com/oval-group/smooth-topk.git
cd smooth-topk
python setup.py install

When done running experiments, to deactivate the environment:

conda deactivate clam

Please report any issues in the public forum.

Using .svs files:

Note that CLAM uses openslide, which relies on the pixman library, and pixman version 0.38 has a known glitch that causes certain downsamples of some .svs files to be read incorrectly. See here for examples, discussion and possible workarounds (the exact solution might differ depending on how your conda environment is setup).

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