Installation

Here you will find a detailed guide on how to install Cell-ACDC. In general, you should be fine with installing the stable version, however, Cell-ACDC development is still quite rapid and if you want to try out the latest features we recommend installing the latest version. On the other hand, installing from source is required only if you plan to contribute to Cell-ACDC development. In that case see this section How to contribute to Cell-ACDC.

Tip

If you are new to Python or you need a refresher on how to manage scientific Python environments, I highly recommend reading this guide by Dr. Robert Haase.

• Install stable version

• Install latest version

• Install from source

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 app.

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, Cell-ACDC 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 Cell-ACDC with the following command:

   pip install "cellacdc"
   

   This tells pip to install Cell-ACDC.

8. Install the GUI libraries:

   After successful installation, you should be able to run Cell-ACDC with 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
   

Updating to the latest stable version of Cell-ACDC

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

pip install --upgrade cellacdc

Install latest 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 app.

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, Cell-ACDC 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 Cell-ACDC directly from the GitHub repo with the following command:

   pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
   

   Tip

   If you already have the stable version and you want to upgrade to the latest version run the following command instead:

   pip install --upgrade "git+https://github.com/SchmollerLab/Cell_ACDC.git"
   

   This tells pip to install Cell-ACDC.

   Important

   On Windows, if you get the error ERROR: Cannot find the command 'git' you need to install git first. Close the terminal and install it from here. After installation, you can restart from here, but remember to activate the acdc environment first with the command conda activate acdc.

8. Install the GUI libraries:

   After successful installation, you should be able to run Cell-ACDC with 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
   

Updating to the latest version of Cell-ACDC

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

pip install --upgrade "git+https://github.com/SchmollerLab/Cell_ACDC.git"

Install from source (developer version)

If you want to try out experimental features (and, if you have time, maybe report a bug or two :D), you can install the developer version from source as follows:

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. Clone the source code with the following command:

   git clone https://github.com/SchmollerLab/Cell_ACDC.git
   

   Important

   On Windows, if you get the error ERROR: Cannot find the command 'git' you need to install git first. Close the terminal and install it from here. After installation, you can restart from here, but remember to activate the acdc environment first with the command conda activate acdc.

4. Navigate to the Cell_ACDC folder with the following command:

   cd Cell_ACDC
   

   The command cd stands for “change directory” and it allows you to move between directories in the terminal.

5. Update conda with the following command:

   conda update conda
   

   This will update all packages that are part of conda.

6. 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.

7. 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.

8. Update pip with the following command:

   python -m pip install --upgrade pip
   

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

9. Install Cell-ACDC with the following command:

   pip install -e "."
   

   The . at the end of the command means that you want to install from the current folder in the terminal. This must be the Cell_ACDC folder that you cloned before.

10. Install the GUI libraries:

    After successful installation, you should be able to run Cell-ACDC with 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
    

Updating Cell-ACDC installed from source

To update Cell-ACDC installed from source, open a terminal window, navigate to the Cell-ACDC folder with the command cd Cell_ACDC and run git pull.

Since you installed with the -e flag, pulling with git is enough.