This software package is designed to automate manual processes, create reusable functions from code, and apply efficient data-cleaning methodologies. It aims to analyze microglia cells, particularly data from the Nance Lab, providing a robust and continuous integration of new functionalities.
The main purpose of this software package is to replace hard-coded chunks of code with callable functions, thus enhancing readability, reusability, and automation. It works in tandem with other repositories from the Nance Lab, including cellmorphflows, diff_viz, microFIBER, and vampire-analysis, focusing on data cleaning, ingestion, and analysis.
The software package can be applied to different datasets but is initially designed to analyze microglia cells from the Nance Lab.
- Clone the Repository: Clone this repository to your local machine.
- Install Dependencies: Run
pip install -r requirements.txtto install the necessary dependencies. - Configure Initial Path: The only manual input required is the initial path for the directory with images.
- Run Main Script: Execute
main.pyto initiate the process.
- main.py: Entry point of the package. Calls directory with images and initiates the workflow.
- data_processing.py: Module for all functions related to image data processing.
- functions.py: Contains reusable functions used across the project.
- visualization.py: Handles plots and data visualizations.
- config.py or settings.yaml: Manages configurations and parameters used across the project.
- requirements.txt: Lists all project dependencies.
- tests/: Holds all test files for unit and integration testing.
This project aligns with the goals of the Nance Lab at the University of Washington, which focuses on nanotechnology as a probe and therapeutic delivery vehicle to treat the diseased brain. Learn more about the Nance Lab.
- cellmorphflows: Contains Jupyter Notebooks for cell morphology quantification.
- diff_viz: Enables quick data visualization for Multiple Particle Tracking (MPT).
- microFIBER: Includes analysis pipelines for the microFIBER paper.
- vampire-analysis: A Python package for cell and nucleus morphology quantification.