The documentation is deployed at Using CellProfiler
This guide demonstrates how to use the CellProfiler Python API to analyze data stored in IDR or in another OMERO server.
This repository contains documentation and notebooks.
The OMERO server used will need to have websockets support enabled.
Alternatively, if you have Docker installed, you can use the repo2docker tool to run this repository as a local Docker instance:
$ git clone https://github.com/ome/omero-guide-cellprofiler
$ cd omero-guide-cellprofiler
$ repo2docker .
Finally, if you would like to install the necessary requirements locally, we suggest using conda.
Then, create the environment:
$ git clone https://github.com/ome/omero-guide-cellprofiler
$ cd omero-guide-cellprofiler
$ conda env create -n omero-guide-cellprofiler -f binder/environment.yml
and activate the newly created environment:
$ conda activate omero-guide-cellprofiler
The following steps are only required if you want to run the notebooks
- If you have Anaconda installed:
- Start Jupyter from the Anaconda-navigator
- In the conda environment, run
conda install ipykernel
- To register the environment, run
python -m ipykernel install --user --name omero-guide-cellprofiler
- Select the notebook you wish to run and select the
Kernel>Change kernel>Python [conda env:omero-guide-cellprofiler]
orKernel>Change kernel>omero-guide-cellprofiler
- If Anaconda is not installed:
- In the environment, install
jupyter
e.g.pip install jupyter
- Add the virtualenv as a jupyter kernel i.e.
ipython kernel install --name "omero-guide-cellprofiler" --user
- Open jupyter notebook i.e.
jupyter notebook
and select theomero-guide-cellprofiler
kernel or[conda env:omero-guide-cellprofiler]
according to what is available
- In the environment, install
An additional benefit of installing the requirements locally is that you can then use the tools without needing to launch Jupyter itself.
See also setup.rst
This is a Sphinx based documentation. If you are unfamiliar with Sphinx, we recommend that you first read Getting Started with Sphinx.