3DCellScope is an advanced 3D image analysis platform using AI-driven segmentation to quantify morphological and topological changes in 3D cell cultures. It analyzes nuclear, cytoplasmic, and organoid-level features, providing insights into tissue patterning and cell organization, with applications in biomedical research and regenerative medicine.
Ensure that your Python version is 3.9.13. The code may not work with Python 3.10 or higher without additional modifications, so please avoid using those versions.
Unzip the folder containing the code and navigate to the project directory.
It is highly recommended to use a virtual environment to prevent conflicts if you're working on multiple Python projects. You can create and activate a virtual environment using the following steps:
To create a virtual environment, run the following command:
virtualenv name_of_your_venv
If your default Python version is not 3.9, you can specify the correct version explicitly:
virtualenv -p python3.9 name_of_your_venv
Once the virtual environment is created, activate it with the appropriate command:
On Windows:
name_of_your_venv\Scripts\activate
After activating the virtual environment, install the required dependencies by running:
pip install -r requirements.txt
The installation process might take a few minutes, but you should not encounter any warnings or errors.
To launch the software, execute the following script:
python OS_Demo.py
Ensure that the virtual environment is activated before running the script.