User Guide

This section provides comprehensive documentation on how to use BactoVision for annotating and analyzing bacterial growth images.

Overview

BactoVision is designed with a focus on usability and flexibility. It provides both automatic and manual annotation capabilities, allowing researchers to quickly process large numbers of images while maintaining the ability to make fine-grained adjustments when needed.

The widget interface is divided into several functional areas:

1. Preprocessing Controls - Tools for enhancing image quality before annotation
2. Grid Controls - Options for configuring the analysis grid
3. Manual Annotation Tools - Brushes and eraser tools for direct annotation
4. Automatic Annotation - Algorithms for automated detection of bacterial colonies
5. Canvas - The main viewing and interaction area

Basic Workflow

A typical workflow using BactoVision follows these steps:

1. Load an image - Create a BactoWidget with your bacterial growth image
2. Adjust the grid - Set up the grid to match your experimental design (or load the configured grid if the images share the same geometry)
3. Preprocess the image - Enhance contrast and other properties if needed
4. Annotate - Use automatic methods and refine with manual tools
5. Extract data - Get quantitative measurements from your annotations

Guides

Detailed information about each aspect of BactoVision is available in the following guides:

• Basic Usage - Getting started with BactoVision
• Grid System - Setting the grid
• Annotations - Methods for annotating bacterial colonies
• Metrics - Available metrics for analysis

Need Help?

If you encounter any issues or have questions about using BactoVision, please open an issue on our GitHub repository.