Levitan Lab ImageJ Plugin Collection

Isee Reader

Author: Arvonn Tully (tully at abtech.org )

History: 2004/04/13: First Released version

Source: Isee_Reader.java

Installation: Download Isee_Reader.class to the plugins folder and restart ImageJ.

Description: This plugin opens Inovison 16 bpp grayscale images. When used in conjunction with the HandleExtraFileTypes pluging listed below, it will open files ending in the ".ise" ending.

HandleExtraFileTypes

Author: Gregory Jefferis (jefferis at stanford.edu)
modified 2004/04/13 by Arvonn Tully (tully at abtech.org )

History: 2004/04/13: Modified Version for use with Isee_Reader.java for Inovison/IseeImaging users

Source: HandleExtraFileTypes.java

Installation: Download HandleExtraFileTypes.class to the plugins folder and restart ImageJ.

Description: I have added a few lines of code to Gregory Jefferies HandleExtraFileTypes code, so that it would recognize *.ise files, and open them with the Isee_Reader plugin which I have supplied above. This enables multiple files to be opened at once with the File_Opener plugin, or the using the JFileChooser. I suggest installing the mmv utility to rename the extensionless Isee files to the ".ise" ending which this plugin recognizes.

Correlation Coefficent Calculator

Author: Arvonn Tully (tully at abtech.org)

History: 2004/04/13: First Released Version

Source: CC_calc.java

Installation: Download CC_calc.class to the plugins folder and restart ImageJ.

Requires: ImageJ version 1.32c or later.

Description: This plugin calculates a pixel by pixel correlation coefficent of an ROI, between 16 bit grayscale images in a stack. It can also calculate the autocorrelation coefficent, essentially a lag analysis of the correlation coefficent's calculated in an image stack. The three checkboxes are sucessively conditional upon selection of the previous check box. That is, if you don't select the previous check box, the sucessive one has no effect. You must select a region of interest, which may anyshape. Failure to provide valid input should produce an error which will inform you of what you didn't do correctly. I have some reservations about the standard error producing code, and I would appreciate some commentary as to wether or not it is correct, and what I should do to correct it. I would also like some feed back as to improving the usefulness of the ploting function.

Or the all in one file, simply extract into your ImageJ directory, and restart ImageJ.

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Author:	Arvonn Tully (tully at abtech.org )

History:	2004/04/13: First Released version
Source:	Isee_Reader.java
Installation:	Download Isee_Reader.class to the plugins folder and restart ImageJ.
Description:	This plugin opens Inovison 16 bpp grayscale images. When used in conjunction with the HandleExtraFileTypes pluging listed below, it will open files ending in the ".ise" ending.

Author:	Gregory Jefferis (jefferis at stanford.edu) modified 2004/04/13 by Arvonn Tully (tully at abtech.org )

History:	2004/04/13: Modified Version for use with Isee_Reader.java for Inovison/IseeImaging users
Source:	HandleExtraFileTypes.java
Installation:	Download HandleExtraFileTypes.class to the plugins folder and restart ImageJ.
Description:	I have added a few lines of code to Gregory Jefferies HandleExtraFileTypes code, so that it would recognize *.ise files, and open them with the Isee_Reader plugin which I have supplied above. This enables multiple files to be opened at once with the File_Opener plugin, or the using the JFileChooser. I suggest installing the mmv utility to rename the extensionless Isee files to the ".ise" ending which this plugin recognizes.

Author:	Arvonn Tully (tully at abtech.org)

History:	2004/04/13: First Released Version
Source:	CC_calc.java
Installation:	Download CC_calc.class to the plugins folder and restart ImageJ.
Requires:	ImageJ version 1.32c or later.
Description:	This plugin calculates a pixel by pixel correlation coefficent of an ROI, between 16 bit grayscale images in a stack. It can also calculate the autocorrelation coefficent, essentially a lag analysis of the correlation coefficent's calculated in an image stack. The three checkboxes are sucessively conditional upon selection of the previous check box. That is, if you don't select the previous check box, the sucessive one has no effect. You must select a region of interest, which may anyshape. Failure to provide valid input should produce an error which will inform you of what you didn't do correctly. I have some reservations about the standard error producing code, and I would appreciate some commentary as to wether or not it is correct, and what I should do to correct it. I would also like some feed back as to improving the usefulness of the ploting function.