Install stable version

1. Install Anaconda or Miniconda

   Anaconda is the standard package manager for Python in the scientific community. It comes with a GUI for user-friendly package installation and management. However, here we describe its use through the terminal. Miniconda is a lightweight implementation of Anaconda without the GUI.

2. Open a terminal

   Roughly speaking, a terminal is a text-based way to run instructions. On Windows, use the Anaconda prompt, you can find it by searching for it. On macOS or Linux you can use the default Terminal.

3. Update conda by running the following command:

   conda update conda
   

   This will update all packages that are part of conda.

4. Create a virtual environment with the following command:

   conda create -n acdc python=3.10
   

   This will create a virtual environment, which is an isolated folder where the required libraries will be installed. The virtual environment is called acdc in this case.

5. Activate the virtual environment with the following command:

   conda activate acdc
   

   This will activate the environment and the terminal will know where to install packages. If the activation of the environment was successful, this should be indicated to the left of the active path (you should see (acdc) before the path).

   Important

   Before moving to the next steps make sure that you always activate the acdc environment. If you close the terminal and reopen it, always run the command conda activate acdc before installing any package. To know whether the right environment is active, the line on the terminal where you type commands should start with the text (acdc), like in this screenshot:

   WindowsmacOS

   

   Anaconda Prompt after activating the acdc environment with the command conda activate acdc.

6. Update pip with the following command:

   python -m pip install --upgrade pip
   

   While we could use conda to install packages, SpotMAX is not available on conda yet, hence we will use pip. Pip the default package manager for Python. Here we are updating pip itself.

7. Install SpotMAX with the following command:

   pip install "spotmax"
   

   This tells pip to install SpotMAX.

8. Install the GUI libraries:

   If you plan to use the SpotMAX GUI and you never used Cell-ACDC before, run the command acdc. Remember to always activate the acdc environment with the command conda activate acdc every time you open a new terminal before starting Cell-ACDC.

   The first time you run Cell-ACDC you will be guided through the automatic installation of the GUI libraries. Simply answer y in the terminal when asked.

   At the end you might have to re-start Cell-ACDC.

   See also

   If you prefer to install the GUI libraries manually, these are the pacakges required:

   condapip

   conda install -c conda-forge pyqt
   conda install -c conda-forge qtpy
   conda install -c conda-forge pyqtgraph
   conda install -c conda-forge seaborn
   conda install -c conda-forge pytables
   

Optional: install Numba

SpotMAX can take advantage of multiple CPU cores using the package numba. For more details, see the Numba documentation.

This typically increases execution speed. After installing SpotMAX, consider installing numba with the following command:

condapip

conda install numba

Note

You can set the number of CPU cores used by numba in the INI configuration file using the Number of threads used by numba parameter as follows:

Updating to the latest stable version of SpotMAX

To update to the latest version of SpotMAX, open the terminal, activate the acdc environment with the command conda activate acdc and the run the follwing command:

pip install --upgrade spotmax