Scaffold Analyser
Application for scaffold analysis. Application algorithm details can be found here
You may want to use it with Hamamatsu NDP Viewer
Install Conda and check "Add Anaconda to my PATH environment variable"
Run in terminal:
conda create -n scaffan -c mjirik -c bioconda -c conda-forge pip scaffan pywin32 python=3.6
activate scaffan
pip install openslide-python imagecodecs tensorflow
python -m scaffan install
python -m scaffan
The pywin32 is used for icon installation. It can be skipped.
conda install -c mjirik -c bioconda -c conda-forge openslide-python scaffan
activate scaffan
conda install -c mjirik -c bioconda -c conda-forge -y scaffan
activate scaffan
python -m scaffan
conda remove --name scaffan --all
There are two problems with openslide (not with openslide-python) package on windows.
- The package is not in conda channel. This is solved by automatic download of the dll binaries.
- Dll binaries cannot be used together with libxml. There is workaround in scaffan. It uses subprocess call to process separately image data and image annotations.