Tissue Tag: jupyter image annotator
Project description
Tissue Tag jupyter image annotator
General instructions until replaced with something proper
- You basically only need the
tissue_tag.py
file, which you will use to import the relevant functions likeimport tissue_tag as tt
You also need the tutorial notebook https://github.com/nadavyayon/TissueTag/blob/main/Tutorials/image_annotation_tutorial.ipynb - You need to setup an env that has bokeh (https://github.com/bokeh/bokeh) and jupyter-bokeh (https://pypi.org/project/jupyter-bokeh/) installed. This is the trickiest bit sometimes
- When running on farm, you need to set the port (e.g., 5011) you are using to get it plot properly in the correct place Python package to interactively annotate histological images within a Jupyter notebook
installation (partial - only tissue-tag)
installation (complete - imagespot)
Instructions for imagespot env
-
Create a new conda environment:
conda create -n imagespot python=3.9
say 'y' when asked -
activate new environment
conda activate imagespot
-
install scanpy
conda install -c conda-forge scanpy python-igraph leidenalg
-
install jupyter-lab
conda install -c conda-forge jupyterlab
-
install open-cv
pip install opencv-python
6_5) optional - install cellpose
pip install cellpose
pip uninstall torch
conda install pytorch cudatoolkit=11.3 -c pytorch
-
install bokeh
pip install jupyter_bokeh
pip install bokeh
-
install scikit-image
pip install scikit-image
-
add the new enviroment to jupyter lab path
$ ipython kernel install --name imagespot --user
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