Summary: This method is appropriate for edge detection of particles in microscopy images. It is less accurate than the Canny edge detection algorithm but requires 48% fewer operations, thus this makes it ideal for datasets that consist of a large number of similar images.
In this work we show how you can use the Canny edge detector to create an edge detection training set for classification. Then, we train a logistic regression algorithm based on this data set and we present the edge detection results on the original image and on two similar images.
Open the .ipynb file for a step-by-step implementation of the algorithm and read the pdf report for more details.
The code is saved in an iPython Notebook format. To review it click on the Canny_training_set.ipynb file.
If you want to run the code in your computer you will need to follow the Install and Run instructions.
The TEM particle images here are provided by the Priestley Polymer Laboratory in Princeton.
Features
- Pixel intensity
- Sobel Derivative of Pixel intensity
Target Variable
3. Edge: Each pixel can either be or not be an edge of a particle
This project requires Python 2.7 and the following Python libraries installed:
You will also need to have software installed to run and execute a Jupyter Notebook
If you do not have Python installed yet, it is highly recommended that you install the Anaconda distribution of Python, which already has the above packages and more included. Make sure that you select the Python 2.7 installer and not the Python 3.x installer.
In a terminal or command window, navigate to the top-level project directory that contains this README and run one of the following commands:
ipython notebook Canny_training_set.ipynbor
jupyter notebook Canny_training_set.ipynbThis will open the Jupyter Notebook software and project file in your browser.