Welcome to BioPrograma, a repository curated by Alexandre Bruni Cardoso, Associate Professor at the University of São Paulo. This collection features Jupyter Notebooks and supplementary materials designed to teach bioimage analysis using Python, complementing the content presented on the BioPrograma YouTube channel.
Bioimage analysis is a critical skill in modern biological research, enabling the extraction of meaningful data from complex imaging datasets. This repository provides hands-on tutorials and code examples to guide learners through various bioimage analysis techniques using Python. The content aligns with the tutorials available on the BioPrograma YouTube channel, offering a comprehensive learning experience.
-
Install Dependencies:
- Some notebooks include environment files (e.g.,
.ymlor.txt) specifying required packages. Locate these files corresponding to the notebook you wish to use and install the dependencies accordingly. For example:conda env create -f environment.yml conda activate bioimage-analysis
- Alternatively, install general dependencies using pip:
pip install -r requirements.txt
- Some notebooks include environment files (e.g.,
-
Launch Jupyter Notebook:
jupyter notebook
Navigate to the desired notebook in your web browser to begin.
Each Jupyter Notebook in this repository focuses on a specific aspect of bioimage analysis, ranging from image preprocessing to advanced segmentation techniques. The notebooks are designed to be self-contained, providing the necessary theoretical background along with practical code examples.
To make the most of these resources:
-
Follow Along with the YouTube Tutorials: Each notebook corresponds to a video tutorial on the BioPrograma YouTube channel. Watching the videos can provide additional context and explanations.
-
Engage with the Code: Modify the code snippets, experiment with different parameters, and observe how the results change. This hands-on approach will deepen your understanding of bioimage analysis techniques.
-
Stay Updated: New notebooks and materials are added regularly. Keep your local repository up to date by pulling the latest changes:
This project is licensed under the BSD 3-Clause License. See the LICENSE file for details.
For questions, suggestions, or further information, feel free to reach out:
- GitHub: brunicardoso
- YouTube: BioPrograma Channel
Your feedback and engagement are invaluable in improving and expanding the resources provided by BioPrograma. Happy analyzing!
Note: This README template is designed to be informative and welcoming, following best practices for GitHub repositories. It provides clear instructions for users to get started, encourages community contributions, and maintains a professional and approachable tone.