fibsem_segm

Segmentation of volume EM data

Using jupyterhub to view data

Go to jupyterhub.embl.de Choose
Image Analysis GPU Desktop

Fiji, ilastik, napari, CellPose. 8 CPU, 16G GPU P100, and 64G RAM

Set up environment for correcting segmentations

Install miniconda: https://docs.conda.io/en/latest/miniconda.html#linux-installers

    cd ~
    wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
    bash Miniconda3-py39_4.11.0-Linux-x86_64.sh 

Then follow what the installer says.
Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] - yes

For correction of labels we will need napari and z5py libraries.