resources > pore analysis software

Software for Pore Detection and Analysis in Microscopy

What is this? A simple tool to analyse SEM imagery and to quantitatively characterise a number of features in micrographs, using simple and efficient image processing techniques.

What it does? Binarisation of grayscale images (designed from SEM microscopy) and Image Analysis of binarised image.

How should I use it? The software comes as a plugin for the ImageJ software. Two commands are provided: BinariseSEM and ComputeStats. You should run BinariseSEM on your SEM micrograph to get a binary image where pores are separated from matrix. The, using ComputeStats you can compute several useful statistics about pores on the binarised image.

How should I install it? Download the gijLib library and the plugin. Move both JAR files into the plugins folder of ImageJ. When you re-start ImageJ the software should be listed in the plugins > gij PoreAnalysis menu. Please, feel free to contact me for any question you may have.
Update. On some systems the JAR files might not work. If this is your case, unzip both files and put the contents into the plugins folder of ImageJ (you may want to create a folder named "gij_PoreAnalysis" and unzip the contents of the plugin - not the library - there).

How should I cite it? If you find my software useful for your work, please cite gijPoreanalysis in your publications, as shown at the bottom of this page.


Installation notes for non-standard ImageJ installations

If you do not use a standard installation of ImageJ (e.g., Fiji or a 64-bit version) binary files might not work. In that case, download the source files for the plugin and the library, unzip them and put the contents in the plugins folder. Then run imageJ and click on Compile and Run ... in the Plugins menu. Open the folder gij_PoreAnalysis in the plugins folder and choose one of the JAVA files. Do this again for each JAVA file in that folder.

Related publications