setup.md

Running the notebooks

Running on cloud resources

Running locally

Finally, if you would like to install the necessary requirements locally, we suggest using Mamba:

• If you do not have any pre-existing conda installation, install Mamba and use mambaforge.
• In case you have a pre-existing conda installation, you can install Mamba by either:
  • Using the recommended way to install Mamba from mambaforge. This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g. /Users/USER_NAME/opt/anaconda3/envs/) then the new mamba envs (e.g. /Users/USER_NAME/mambaforge/envs/). You can verify this by running conda env list. The addition of export CONDA_ENVS_PATH=/Users/user/opt/anaconda3/envs/ into your .bashprofile or .zprofile file will fix this.
  • Use the Existing conda install way, i.e. run conda install mamba -n base -c conda-forge whilst in the base environment. This way can take much longer time than the recommended way described above, and might not lead to a successful installation, especially if run on arm64 (Apple Silicon) OS X.

To avoid conflict with used packages, we have prepared several environments: Day_4/environment_cellpose.yml, Day_4/environment_basic.yml, Day_4/environment_public.yml and Day_4/environment_cp.yml

Create the environments. For this, first run the commands below as written, then replace Day_4/environment_cellpose.yml with Day_4/environment_basic.yml or Day_4/environment_cp.yml and run again to create the other envs:

For Windows, OS X x86_64 (NOT arm64 Apple Silicon), Linux:

$ git clone https://github.com/ome/EMBL-EBI-imaging-course-04-2024

$ cd EMBL-EBI-imaging-course-04-2024

$ mamba env create -f Day_4/environment_cellpose.yml

For OS X arm64 Apple Silicon

$ git clone https://github.com/ome/EMBL-EBI-imaging-course-04-2024   

$ cd EMBL-EBI-imaging-course-04-2024

$ CONDA_SUBDIR=osx-64 mamba env create -f Day_4/environment_cellpose.yml

and activate the newly created environment:

$ conda activate imaging_course_cellpose_day4_2024

Before creating a new environment, remember to deactivate the current one:

$ conda deactivate

See also Conda command reference.

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 mamba install ipykernel (for OS X Apple Silicon CONDA_SUBDIR=osx-64 mamba install ipykernel)
  • To register the environment, run python -m ipykernel install --user --name imaging_course_cellpose_day4_2024
  • Select the notebook you wish to run and select the Kernel>Change kernel>Python [conda env:imaging_course_cellpose_day4_2024] or Kernel>Change kernel>imaging_course_cellpose_day4_2024

• If Anaconda is not installed:

  • Add the virtualenv as a jupyter kernel i.e. ipython kernel install --name "imaging_course_cellpose_day4_2024" --user
  • Open jupyter notebook i.e. jupyter notebook and select the imaging_course_cellpose_day4_2024 kernel or [conda env:imaging_course_cellpose_day4_2024] according to what is available.

  To stop the notebook server, in the terminal where te server is running, press Ctrl C. The following question will be asked in the terminal Shutdown this notebook server (y/[n])?. Enter the desired choice.