Basic Usage

This guide covers the fundamental operations for using BactoVision to analyze bacterial growth images.

Getting Started

To begin using BactoVision, you need to import the main widget class and create an instance with your image:

from bactovision.widget import BactoWidget

# Create a widget with an image
widget = BactoWidget('path/to/your/image.png')

Loading Images

BactoVision supports various ways to load images:

# From a file path
widget = BactoWidget('path/to/image.png')

# optionally, one can also provide the grid configuration path:

widget = BactoWidget('path/to/image.png', grid_config='path/to/grid_config.json')

# From a NumPy array
import numpy as np
from PIL import Image

img = np.array(Image.open('path/to/image.png'))
widget = BactoWidget(img)

Grid

Next, one should set the Grid - either manually or by providing the path to the saved grid configuration.

Annotation

See the Annotation page for details on the annotation process.

Save metrics

After annotating the image, extract and save the Metrics.