Bioimage informatics

"PTA2 is an ImageJ1.x plugins that enable automatic particle tracking"

This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background. 

"The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes."

h-Dome transformation, useful for spot detection.

Jython code example:

from de.unihalle.informatik.MiToBo.core.datatypes.images import MTBImage
from de.unihalle.informatik.MiToBo.morphology import HDomeTransform3D
from ij import IJ

imp = IJ.getImage()
mtb = MTBImage.createMTBImage( imp.duplicate() )
hdome = HDomeTransform3D(mtb, 10.0)
hdome.runOp()
mtbdone = hdome.getResultImage()
imp2 = mtbdone.getImagePlus()
imp2.show()

Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org