Cell Binarization tool
Python GUI for manual cell image binarization. Users can manually pick a threshold for a given video and binarize it. Below are the features implemented for this app.
- Ability to select input file name, start frame number, end frame number, and frame interval (used to display frames in the multiple of frame interval)
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Ability to set custom threshold for each page
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To use this feature start by sliding the threshold for page 1. You will see that the threshold for all the following pages change as well.
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Now as you go to page 2. The threshold for page 1 is saved. Changing the threshold now will change it for the current page and all the following pages.
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Keep going through all the pages to select the threshold for each. The threshold for each page can be viewed on the right side of the window.
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- Ability to see recommended threshold. The app uses Otsu's method to come up with a recommended threshold. The number is generated by averaging all the images’ otsu’s threshold.
- Ability to see the histogram. The “Display Histogram” button in red shows the histogram for the top left frame (also in red) shown in the GUI window. In the figure above when a user presses Display Histogram button Frame 390’s histogram will be shown. The histogram will change for each page as the frame on the top left changes. The red vertical line is the threshold chosen by the user for that page.
- Ability to save binarized images. Users can select a folder where they want the binarized images to be saved.
Made at UCI