Texture Analyzer

Texture Analyzer

Author: Julio E. Cabrera (jcabrera at mail.nih.gov)

History: 2003/06/10 (v0.0): First version
2005/06/10 (v0.1): The normalization constant (R in Haralick's paper, pixelcounter here) now takes in account the fact that for each pair of pixel you take in account there are two entries to the grey level co-ocurrence matrix. Changes were made also in the Correlation parameter. Now this parameter is calculated according to Walker's paper.
2006/07/07 (v0.4): Works with stacks and with macros.

Source: GLCM_Texture.java

Installation: Copy GLCM_Texture.class to the plugins folder and restart ImageJ.

Description: This plugin computes several of the texture parameters described by Haralick (Haralick, R. M., Shanmugam, K., and Dinstein, I. (1973). Texture parameters for image classification, IEEE Trans SMC 3, 610-621). The only parameter computed differently is "Correlation", which is now calculated as described by Walker and col. (Walker, R. F., Jackway, P., and Longstaff, I. D. (1995). Improving Co-occurrence Matrix Feature Discrimination. Paper presented at: Third Conference on Digital Image Computing: Techniques and Applications.). Please note that the computations carried out in this plugin are normalized by area (see also below): two ROIs of different size but the same texture will result i n similar results for their texture parameters.
The texture parameters have been used in several areas of the biomedical research, sometimes to diagnose tumors by measuring the textural parameters in the nucleus of cells from biopsies (Murata, S., Herman, P., and Lakowicz, J. R. [2001]. Texture analysis of fluorescence lifetime images of AT- and GC-rich regions in nuclei, J Histochem Cytochem 49, 1443-51)(Murata, S., Herman, P., and Lakowicz, J. R. [2001]. Texture analysis of fluorescence lifetime images of nuclear DNA with effect of fluorescence resonance energy transfer, Cytometry 43, 94-100).
The plug in works with 256 gray level images only. This is because the gray level co-occurrence matrices proposed by Haralick were based in these type of images.
Corrected/added in version 0.1:

Better area normalization. There was a bug in the original plugin that resulted in a deffective normalization procedure. In this new version, the sum of all the members of the GLCM is close to 1.
The sum of all the members of the GLCM is displayed in the "Results" window. The value of this sum should be close to 1 and provides a control to ensure that the calculations have proceeded without problems.
Known issues:

The plug in works computes square ROIs only. Even when it works with multi-shaped ROIs, it always computes a square region based on those ROIs. I'm working on a new version that will support non-rectangular ROIs.
When called within a macro, the plugin doesn't return any calculations. I'm working on a fix for this and will have the updated version ready soon.
When no ROI is selected and the "size of the step in pixels" is greater than 5, the plugin returns texture parameter values but several errors are reported in a separate window. I encourage the users to use ROIs when using the plugin as I work on a solution to this problem.
Disclaimer:
Since I am an amateur programmer, I wrote this plug in based in the "programming examples" of the ImageJ website. All through the code, you will find shells and methods that have been borrowed from such examples. I hope this is not a problem.

See Also: The Batch GLCM Measure macro is a wrapper for this plugin that allows batch processing of all the images in a directory.

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Author:	Julio E. Cabrera (jcabrera at mail.nih.gov)
History:	2003/06/10 (v0.0): First version 2005/06/10 (v0.1): The normalization constant (R in Haralick's paper, pixelcounter here) now takes in account the fact that for each pair of pixel you take in account there are two entries to the grey level co-ocurrence matrix. Changes were made also in the Correlation parameter. Now this parameter is calculated according to Walker's paper. 2006/07/07 (v0.4): Works with stacks and with macros.
Source:	GLCM_Texture.java
Installation:	Copy GLCM_Texture.class to the plugins folder and restart ImageJ.
Description:	This plugin computes several of the texture parameters described by Haralick (Haralick, R. M., Shanmugam, K., and Dinstein, I. (1973). Texture parameters for image classification, IEEE Trans SMC 3, 610-621). The only parameter computed differently is "Correlation", which is now calculated as described by Walker and col. (Walker, R. F., Jackway, P., and Longstaff, I. D. (1995). Improving Co-occurrence Matrix Feature Discrimination. Paper presented at: Third Conference on Digital Image Computing: Techniques and Applications.). Please note that the computations carried out in this plugin are normalized by area (see also below): two ROIs of different size but the same texture will result i n similar results for their texture parameters. The texture parameters have been used in several areas of the biomedical research, sometimes to diagnose tumors by measuring the textural parameters in the nucleus of cells from biopsies (Murata, S., Herman, P., and Lakowicz, J. R. [2001]. Texture analysis of fluorescence lifetime images of AT- and GC-rich regions in nuclei, J Histochem Cytochem 49, 1443-51)(Murata, S., Herman, P., and Lakowicz, J. R. [2001]. Texture analysis of fluorescence lifetime images of nuclear DNA with effect of fluorescence resonance energy transfer, Cytometry 43, 94-100). The plug in works with 256 gray level images only. This is because the gray level co-occurrence matrices proposed by Haralick were based in these type of images. Corrected/added in version 0.1: Better area normalization. There was a bug in the original plugin that resulted in a deffective normalization procedure. In this new version, the sum of all the members of the GLCM is close to 1. The sum of all the members of the GLCM is displayed in the "Results" window. The value of this sum should be close to 1 and provides a control to ensure that the calculations have proceeded without problems. Known issues: The plug in works computes square ROIs only. Even when it works with multi-shaped ROIs, it always computes a square region based on those ROIs. I'm working on a new version that will support non-rectangular ROIs. When called within a macro, the plugin doesn't return any calculations. I'm working on a fix for this and will have the updated version ready soon. When no ROI is selected and the "size of the step in pixels" is greater than 5, the plugin returns texture parameter values but several errors are reported in a separate window. I encourage the users to use ROIs when using the plugin as I work on a solution to this problem. Disclaimer: Since I am an amateur programmer, I wrote this plug in based in the "programming examples" of the ImageJ website. All through the code, you will find shells and methods that have been borrowed from such examples. I hope this is not a problem.
See Also:	The Batch GLCM Measure macro is a wrapper for this plugin that allows batch processing of all the images in a directory.