MorphoGlia has been developed with a focus on user-friendliness and accessibility, making it an ideal tool for the broader scientific community. The software is available in two main modes: a software mode and an interface mode, both designed to facilitate ease of use. The executable file was generated using PyInstaller (https://pyinstaller.org/en/stable/), while the interactive interface was built using the Tkinter Python library (https://docs.python.org/3/library/tkinter.html). For advanced users, direct modification of the source code is recommended to tailor the application to the specific needs of individual experiments. This approach allows for greater flexibility and customization, ensuring that MorphoGlia can be adapted to a wide range of research scenarios.
To use the interface mode, download the MorphoGlia_Interface directory. You can run it from the terminal or through a Python interface. Ensure that the files MorphoGlia_app.py and morphoglia.py are located in the same directory. You will need to install the necessary libraries.
The executable mode is available for download at the following link: https://drive.google.com/drive/u/1/folders/15Mu2THZvVH6OTlDZuzf7ftsWyLAiWjUV
The source code is located in the MorphoGlia_code directory. This directory includes the interactive mode for point tracking, color mapping to customize cluster colors, and the R and Python scripts needed to reproduce the graphics.
Also, check out the video "MorphoGlia Tutorial" on YouTube for an example of how to use the MorphoGlia software: https://www.youtube.com/watch?v=OLLS9I8ln48&t=17s
Currently, the software is available for Macs with M1/M2 processors. We are working on versions for Intel-based Macs and Windows.
Ensure you have Python 3.10.14 installed. You can use a terminal or an Integrated Development Environment (IDE) such as Spyder, PyCharm, or Visual Studio.
To ensure compatibility, install the following libraries and verify their versions:
#One-step installation:
conda env create -f morphoglia.yml
#Manual Installation:
#If you encounter issues with the one-step installation, install each library individually:
# Install OpenCV (version 4.10.0)
conda install -c conda-forge opencv=4.10.0
python -c "import cv2; print(cv2.__version__)" # Verify installation (expected version: 4.10.0)
# Install Pandas (version 2.2.2)
pip install pandas==2.2.2
python -c "import pandas as pd; print(pd.__version__)" # Verify installation (expected version: 2.2.2)
# Install TiffFile (version 2024.8.10)
pip install tifffile==2024.8.10
python -c "import tifffile; print(tifffile.__version__)" # Verify installation (expected version: 2024.8.10)
# Install Scikit-Image (version 0.24.0)
pip install scikit-image==0.24.0
python -c "import skimage; print(skimage.__version__)" # Verify installation (expected version: 0.24.0)
# Install Matplotlib (version 3.9.2)
pip install matplotlib==3.9.2
python -c "import matplotlib; print(matplotlib.__version__)" # Verify installation (expected version: 3.9.2)
# Install Scikit-Learn (version 1.5.1)
pip install scikit-learn==1.5.1
python -c "import sklearn; print(sklearn.__version__)" # Verify installation (expected version: 1.5.1)
# Install Seaborn (version 0.13.2)
pip install seaborn==0.13.2
python -c "import seaborn as sns; print(sns.__version__)" # Verify installation (expected version: 0.13.2)
# Install UMAP-learn (version 0.5.6)
pip install umap-learn==0.5.6
python -c "import umap; print(umap.__version__)" # Verify installation (expected version: 0.5.6)
# Install HDBSCAN (version 0.8.38.post1)
pip install hdbscan==0.8.38.post1
pip show hdbscan | grep Version # Verify installation (expected version: 0.8.38.post1)
# Install Datashader (version 0.16.3)
pip install datashader==0.16.3
pip show datashader | grep Version # Verify installation (expected version: 0.16.3)
# Install Bokeh (version 3.5.1)
pip install bokeh==3.5.1
pip show bokeh | grep Version # Verify installation (expected version: 3.5.1)
# Install HoloViews (version 1.19.1)
pip install holoviews==1.19.1
pip show holoviews | grep Version # Verify installation (expected version: 1.19.1)
a) Open the MorphoGlia-main folder and move the MorphoGlia_Interface folder to your Desktop.
b) Open your terminal and navigate to the directory containing the Morphoglia_Interface files. For example:
Locate on the directory "Morphoglia_Interface". For example:
cd Desktop/Morphoglia_Interfacec) Run the interface using the following command:
python Morphoglia_app.pyThis will start and display the interface mode.
Alternatively, you can run the interface from a Python IDE by opening the Morphoglia_app.py file and executing it.