Quantify the Area of synpatophysin staining after masking out the thioflavin staining.

Image Quantification:
Subtract Thioflavin Stains from Synaptophysin
Author: Ricky Savjani, Angie Chiang
Contact: savjani@bcm.edu
Created: 9/23/2012

Prep:
1.) Save all images into same folder
2.) use a distinct flag for thioflavin for each thioflavin image
    (e.g. 'thio' in 'img_2_1_thio.tif')
2.) use a distinct flag for synaptophysin for each synaptophysin image
    (e.g. 'synapto' in 'img_2_1_synapto.tif')

Example Usage:

[outputMat] = SynaptophysinQuantification();

Input Prompts:
1.) Input image directory of all image files
2.) Output directory to save CSV file and all image files
3.) Thioflavin flag: A Flag to differentiate thioflavin images in the
input directory
4.) Synpatophysin flag: A Flag to differentiate thioflavin images in the
input directory

Outputs:
1.)
outputMat: outputMat is a 3 column cell matix:
Column 1: Name of Brain
Column 2: Mean Masked Intensity
Column 3: Percent Area staining positive for Synaptophysin
Also writes the outputMat to a CSV file called 'MaskedVals.csv'

2.)
Saves all the Synaptophysin Minus Thioflavin B&W Tiff images