Installation

This guide contains instructions for installing Cell-ACDC in different ways. In the future a video will be added.

Installation using Anaconda (recommended)

1. Install Anaconda or Miniconda (make sure to use the 64-bit version for Windows)

   Anaconda is a distribution of Python, which helps with package management and simplifies many aspects of using Python. Python is a programming language and needs an interpreter to function. Miniconda is a lightweight implementation of Anaconda.

2. Open the terminal (for Windows use the anaconda terminal)

   A terminal is a text-based way to communicate with the computer. The anaconda terminal is a terminal specifically for anaconda, with some commands specific to anaconda only available there.

3. Update conda by typing conda update conda

   This will update all programmes (or packages) that are part of conda.

4. Create a virtual environment by typing conda create -n acdc python=3.9

   This will create a virtual environment, which is an isolated instance and partially independent from the rest of the system. The virtual environment is called acdc in this case.

5. Activate the virtual environment by typing conda activate acdc

   This will activate the environment, meaning that the console is now not in the default system environment, but the acdc environment. If the activation of the environment was successful, this should be indicated to the left of the active path, circled in red below.

6. Update pip using python -m pip install --upgrade pip

   Pip is an application which is included in Python. It manages programmes and updates it. In this case, we tell pip to update itself.

7. Install Cell-ACDC using pip install "cellacdc[gui]"

   This tells pip to install Cell-ACDC, specifically the version with an user interface.

Advanced install methods

The following part of the guide is intended for users who are interested in changing Cell-ACDC’s code.

IMPORTANT: Before installing with other methods

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 BEFORE proceeding with Cell-ACDC installation.

Installation using Pip

Windows

1. Download and install Python 3.9. Make sure to check the checkbox so python is added to PATH, as seen in the picture below. This is so you can access python commands from anywhere.

2. Open a terminal. On Windows we recommend using the PowerShell that you can install from here. On macOS use the Terminal app.

3. Upgrade pip: Windows: py -m pip install --updgrade pip, macOS/Unix: python3 -m pip install --updgrade pip

4. Navigate to a folder where you want to create the virtual environment

5. Create a virtual environment: Windows: py -m venv acdc, macOS/Unix python3 -m venv acdc

6. Activate the environment: Windows: .\acdc\Scripts\activate, macOS/Unix: source acdc/bin/activate

7. Install Cell-ACDC with the command pip install "cellacdc[gui]". Note that if you know you are going to need tensorflow (for segmentation models like YeaZ) you can run the command pip install "cellacdc[all]", or pip install tensorflow before or after installing Cell-ACDC.

Install from source

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.

2. Open a terminal and navigate to a folder where you want to download Cell-ACDC. If you are on Windows you need to use the “Anaconda Prompt” as a terminal. You should find it by searching for “Anaconda Prompt” in the Start menu.

3. Clone the source code with the command git clone https://github.com/SchmollerLab/Cell_ACDC.git. If you are on Windows you might need to install git first. Install it from here.

4. Navigate to the Cell_ACDC folder with the command cd Cell_ACDC.

5. Update conda with conda update conda. Optionally, consider removing unused packages with the command conda clean --all

6. Create a new conda environment with the command conda create -n acdc_dev python=3.9

7. Activate the environment with the command conda activate acdc_dev

8. Upgrade pip with the command python -m pip install --upgrade pip

9. Install Cell-ACDC with the 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. OPTIONAL: If you need tensorflow run the command pip install tensorflow.

Updating Cell-ACDC installed from source

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

git pull

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

Install from source with forking

If you want to contribute to the code or you want to have a developer version that is fixed in time (easier to get back to in case we release a bug :D) we recommend forking before cloning:

1. Install Anaconda or Miniconda.

2. Create a personal GitHub account and log in.

3. Go to the Cell-ACDC GitHub page and click the “Fork” button (top-right) to create your own copy of the project.

4. Open a terminal and navigate to a folder where you want to download Cell-ACDC. If you are on Windows you need to use the “Anaconda Prompt” as a terminal. You should find it by searching for “Anaconda Prompt” in the Start menu.

5. Clone the forked repo with the command git clone https://github.com/your-username/Cell_ACDC.git. Remember to replace the your-username in the command. If you are on Windows you might need to install git first. Install it from here.

6. Navigate to the Cell_ACDC folder with the command cd Cell_ACDC.

7. Add the upstream repository with the command git remote add upstream https://github.com/SchmollerLab/Cell_ACDC.git

8. Update conda with conda update conda. Optionally, consider removing unused packages with the command conda clean --all

9. Create a new conda environment with the command conda create -n acdc_dev python=3.9. Note that acdc_dev is the name of the environment and you can call it whatever you like. Feel free to call it just acdc.

10. Activate the environment with the command conda activate acdc_dev

11. Upgrade pip with the command python -m pip install --upgrade pip

12. Install Cell-ACDC with the 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.

13. OPTIONAL: If you need tensorflow run the command pip install tensorflow.

Updating Cell-ACDC installed from source with forking

To update Cell-ACDC installed from source, open a terminal window, navigate to the Cell-ACDC folder and run the command

git pull upstream main

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