Skip to content

Home

Jump to bottom
Steven J. West edited this page Jan 4, 2021 · 18 revisions

Welcome to the Multi-OTSU Segmentation wiki!

User Installation:

  1. Download Multi-OTSU Segmentation.

  2. Move the downloaded JAR to your ImageJ plugins/ directory.

  3. Start ImageJ: The plugin can be found under Plugins > Multi-OTSU Segmentation > Multi-OTSU Segmentation

Usage Guide

The plugin presents an initial dialog, where the numLevels, Background Selection, and stack options can be set:

  • numLevels: Select the number of LEVELS or classes/groups that the multi-OTSU algorithm with use when sorting all pixels into groups.

  • Background Selection: Select the LEVEL up to which the pixels will be considered background pixels. All pixels in levels above this value will be considered segmented pixels.

    • This value should not be at or above the numLevels value - otherwise ALL pixels will be assigned to background.

  • stack: Check this box to run the algorithm on the stack histogram. If unchecked, each slice in a stack is processed separately.

  • log: Check this box to log the segmentation points identified by the segmentation algorithm. If unchecked, no log of data is made (default).

NOTE: This plugin will segment data based on the entire stack - it does not currently split and act on channels or frames separately. The user/programmer must work in each channel/frame independently with this plugin for correct segmentation of each channel/frame.

Example: Blobs

Here, the original blobs image (left) is segmented using numLevels 3, and Background selection of 1 (middle), or 0 (right).

See the original plugin for more detailed description:

https://imagej.net/Multi_Otsu_Threshold

Clone this wiki locally