This plugin can be used to calculate image intensities (mean, min, max or sum) of 3 areas stored under 3 materials of a model.

The results of the plugin may be seen on the screen of Microscopy Image Browser or saved as Excel spreadsheet.


How to Use

This example shows comparison of image intensities between cytosol and nucleus in cells.

The intensities of each object will be calculated and the numbers displayed at the Image View panel. For example in the figure below, intensity of the Background, Nucleus and Cytosol are 142.3671, 340.2101 and 99.7331 correspondingly (please note that the intensity of the background was subtracted from the intensities of other objects). The numbers are stored in the Annotation layer available from the Menu->Models->Annotations. The corresponding objects will also be connected with a line for reference. The line is stored in the Selection layer and can be removed using the Shift+C shortcut.

The results of the analysis are stored in the excel file

Additional Options


Written by Ilya Belevich, University of Helsinki
version 1.00, 15.09.2014
email: ilya.belevich @

Part of the code written by Gunther Struyf was used when writing this function.