Image Quantification:
Subtract Thioflavin Stains from Synaptophysin
Author: Ricky Savjani, Angie Chiang,
Joanna L. Jankowsky
Contact: savjani@bcm.edu
Web: http://neuro.bcm.edu/jankowskylab/
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 |
