🐊 Getting Started with SpatialAE¶
Kindly note that SpatialAE is not a plug-and-play solution. It's a framework that requires significant upfront investment of time from potential users for training and validating deep learning models, which can then be utilized in a plug-and-play manner for processing large volumes of similar multiplexed imaging data.
There are two ways to set it up based on how you would like to run the program
- Using an interactive environment like Jupyter Notebooks
- Using Command Line Interface
Before we set up SpatialAE, we highly recommend using a environment manager like Conda. Using an environment manager like Conda allows you to create and manage isolated environments with specific package versions and dependencies.
Download and Install the right conda based on the opertating system that you are using
Create a new conda environment¶
# use the terminal (mac/linux) and anaconda promt (windows) to run the following command
conda create --name spatialAE -y python=3.10
conda activate spatialAE
Install spatialAE within the conda environment.
pip install spatialAE
Interactive Mode¶
Using IDE or Jupyter notebooks
pip install notebook
# open the notebook and import spatialAE
import spatialae as sa
# Go to the tutorial section to follow along