https://github.com/dnhkng/huang-thresholding

A nice thresholding algorithm for bacterial colony isolation
https://github.com/dnhkng/huang-thresholding

Last synced: 12 days ago
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A nice thresholding algorithm for bacterial colony isolation

• Host: GitHub
• URL: https://github.com/dnhkng/huang-thresholding
• Owner: dnhkng
• Created: 2014-03-24T16:14:31.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2024-02-18T11:15:28.000Z (9 months ago)
• Last Synced: 2024-02-18T12:26:02.851Z (9 months ago)
• Language: Python
• Size: 5.65 MB
• Stars: 9
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Huang-Thresholding

A nice thresholding algorithm for bacterial colony isolation

Implements Huang's fuzzy thresholding method, recoded from the Java version from ImageJ.

Uses Shannon's entropy function, from *Huang L.-K. and Wang M.-J.J. (1995) "Image Thresholding by Minimizing the Measures of Fuzziness" Pattern Recognition, 28(1): 41-51*

### Installation

Copy the python files to your working directory.

### Testing

```Python

python -m unittest test_huang_thresholding.py

```

### Usage 

There are bacterial colonies images in 'colonies.npy'

To calculate the Huang Thresholding, you would use the following code to first get the data into numpy and get the histogram values, and then calculate the threshold.

```Python

import numpy as np

from huang_thresholding import HuangThresholding

colony_data = np.load("colonies.npy")

histogram_data, _ = np.histogram(colony_data, bins=range(257))

huang_thresholding = HuangThresholding(histogram_data)

threshold = huang_thresholding.find_threshold()

```