Nucleus Detection Program 
OLEG POLYAKOV | PRINCETON UNIVERSITY | 2008-2013

This program allows for the manual detection of nucleus in 3-D.
The input for this program is a thresholded stack (X-Y-Z-T) of nucleus
images. It is entered into the handles.imfile path below. One also needs to
enter the parameters of the image, such as the number of Z stacks and the
number of T stakcs.

To generate a thresholded image one usually runs some preprocessing
algorithms on the image, such as a bandpass filter and a gaussian blur
filter. Then a threshold is picked and applied to the image (usually with
ImageJ). 

One can also use the Hessian_Filter function, which is very good for the 3D blur detection.

This program allows you to seperate clumps of nulcei by cutting them
manually using the mouse. When the left button of the mouse is pressed, the
mouse will begin to delete pixels from the data allowing you to seperate
them manually. CAREFUL - the image will automatically be saved, so make
sure you have a backup!!

There are also some useful functions used for Nucleus Processing.

Hessian_Filter: This is a very useful function. It allows you to filter the nucleus data by calculating the 3D Hessian of the image. 