Here are some plugins for ImageJ.
The plugins were written by Jens Bache-Wiig and myself.
The plugins are free software (in the public domain).
except the Susan plugins, which are under a free non-commercial licence,
included in the download.
Java 1.5 or later is required.
To install the plugins, copy the .class files to the ImageJ plugin folder.
To install the Susan smoothing plugin, read the install.txt file.
This is an implementation of 2D and 3D Susan smoothing. When number of depth (z) slices are 1, 2D smoothing is done, else 3D.
Download: [zipfile] [browse files] (Uses 3x image size memory)
Download: c-version (Uses 2x image size memory)
Isolated Pixel Removal
Removes background pixels (black) completely surrounded by foreground pixels (white).
Works on both 2D and 3D images (stack). Treats a stack as a 3D image.
Small Region Removal
Removes regions smaller than a specified threshold.
[a modified version suited for use in macros, courtesy of Georg Fiedler]