cellrake 1.0.0

A Python package for analyzing cells in fluorescent images

CellRake 🔬

Why this package?

CellRake is a Python package that analyzes cells in fluorescent images. It provides tools for image segmentation based on Scikit-image, model training and prediction based on Scikit-learn, and colocalization analysis, tailored for complex experiments involving multiple fluorescent markers.

Installation

Step 1: Install Conda

First, you need to install Conda, a package and environment management system. If you don't have Conda installed, you can download and install it by following these steps:

1. Go to the Miniconda download page.
2. Choose the version for your operating system (Windows, macOS, or Linux).
3. Follow the installation instructions provided on the website.

Miniconda is a minimal version of Anaconda that includes only Conda, Python, and a few essential packages, making it lightweight and easy to manage.

Step 2: Create a Conda Environment

A Conda environment is an isolated space where you can install specific versions of Python and packages, like CellRake, without affecting other projects or installations. This is important to avoid conflicts between different software packages.

To create a new Conda environment for CellRake, open a terminal and run the following commands:

conda create --name cellrake python=3.10

This command creates a new environment named cellrake with Python 3.9 installed.

Step 3: Activate the Conda Environment

Before installing the CellRake package, you must activate the Conda environment you just created. This tells your system to use the Python and packages installed in that environment.

To activate the environment, run:

conda activate cellrake

After running this command, your terminal prompt should change to indicate that you're now working within the cellrake environment.

Step 4: Install CellRake

Now that your environment is set up and activated, you can install CellRake. The package is hosted on PyPI.

To install CellRake, run the following command:

pip install cellrake

This command tells pip to install CellRake from the PyPI repository. Now you are ready to go!

Note: If you installed the package some time ago, I recommend updating to the newest version to avoid bugs. You can do this by running:

pip install cellrake --upgrade

How to use it?

For detailed tutorials and use cases, see the examples directory:

• Training Models: learn how to train a machine learning model using your dataset.
• Analyzing Images: analyze new images using a pre-trained model.

License

CellRake is licensed under the MIT License.