We will be using a yml file to setup our conda environment. Yml files (Yet another Markup Language) files are a quick and easy way to share reproducible environments between image analysts. Remember REPRODUCIBILTY IS KEY IN IMAGE ANALYSIS
We will be using the Crick_IA.yml file to create our segmentation conda installation. The file automatically installs StarDist and CellPose. We will also be using Jupyter Notebooks as our coding environment, so we need to set that up as well.
Let's get started by installing the yml file first
Open up the Anaconda Prompt and navigate to where the environment file (in this case, Crick_IA.yml) is Then, enter this command in the Anaconda prompt:
conda env create -f Crick_IA.yml
Once the environment is created, we need to activate it
conda activate Crick_IA
Now to install remote_ikernel, the kernel manager
pip install remote_ikernel
Once the remote_ikernel is installed, we can link the kernel to jupyter notebooks easily using this command
python -m ipykernel install --user --name=Crick_IA --display-name "Crick_IA"
Now we can open jupyter notebook from the Anaconda prompt using this command:
jupyter notebook
When Jupyter notebooks opens, open a new notebook, and try:
import stardist
import cellpose
If these work, we're doing great!