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ImageJ plugin for Cell Segmentation PDF Print
Article Index
ImageJ plugin for Cell Segmentation
Using the Plugin
Region Analysis
Plugin Configuration
Download and Instalation

This software is designed to process transmission electron microscopy images containing cells. It is implemented as a plugin for ImageJ (image processing and analysis program). It contains semiautomatic tools for segmentation of organelles and allows their analysis. The plugin also supports automatic cell and nucleus segmentation.

The software has been developed in terms of project MUNI/M/1050/2013 and supporded by Grant Agency of Masaryk University.

Input Images

The plugin is designed to process transmission electron microscopy images. The input images must be in TIFF format.  There is an example of an input image:

Example of an input image

Plugin Submenu

Every plugin tool is accesible from the main menu in Plugins->TEM Images. There is a list of tools with a short description:

 

  • Preprocess Images... preprocesses images in a given folder (image size, bit depth) and exports them to another folder
  • Detect Cell and Nucleus... - detects cell and nucleus on every image in a given folder and exports a segmented image to another folder
  • Open Images... – opens a window for browsing images and organelle segmentation
  • Analyze Images... – calculates a group of parameters on images from a given folder



Written by Jan Ježek   
Last Updated ( Tuesday, 16 May 2017 )
 
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