SNAzzy is a Python package for studying synchronous network activity (SNA) in Drosophia embryos via high-thoughput microscopy.
The software includes processing raw data into individual .tif files, quantification of fluorescence and changes in morphology, a custom peak detection algorithm, and a GUI for data visualization and curation.
Refer to the README files inside the snazzy_processing or snazzy_analysis packages for details on running the code.
The project uses conda to manage dependencies. If you don’t already have conda, you can download and install it from the official website.
Make a copy of the repo (e.g. with git clone), then cd into the root folder of the repo.
Recreate the conda environment with the dependencies listed in environment.yml in the repo's root:
conda env create -f environment.yml
Activate the environment:
conda activate snazzy-env
Tests can be run with pytest.
You can run the test suite from the project’s root directory to test everything at once. Make sure the environment is active, and then run:
pytest
Thank you for being interested in snazzy!
We accept contributions of all sorts: improving documentation, submitting bug reports, adding feature requests or writing code. Feel free to create an issue or a pull request!
If you are new to open source and need help creating a pull request, we recommend taking a look at the first-contributions repository.
Please open an issue for any bugs or requests for help analyzing your data.
When filing an issue, please add the following information:
- What operating system are you using?
- What did you expect to see?
- What did you see instead?
Important
For issues related to data analysis, please provide an example dataset.
Please file an issue explaining the desired feature or enhancement.