This app loads tiff images of neuron terminals in footpad saved in a single folder. It then lets the user crop the image by either freehand drawing or polygon. The user can choose a thresholding method, either binary thresholding or Otsu's method and calculates the Innervation index and saves it as a txt file in the same folder. The user can access the intermediate steps from .MAT file saved in same folder.
Steps to follow:
1. Put all your tif or tiff images in a folder
2. Run the .mlapp file
3. In the app window, press on "Load Folder" and browse to select the desired folder
4. Then set the "Cut off Algorithm" to either "1-0 Cut off" or "Otsu"
5. For "1-0 Cut off", enter "Cut off Value" (Cut off value is not normalized. It is shade of gray out of 2^16 = 65536 shades. For example 2500 is 0.0385 on a 0-1 scale of gray.)
6. Choose "Crop Options" between "Polygon" and "Freehand"
7. Press "Calculate"
8. Crop the desired region of interest (ROI) and the app asks whether another fine cropping is needed just for the purpose of noise reduction
9. The innervation index is calculated and is saved in the same folder as a TXT file, where the first column is name of the Image file and the second column is innervation index value
10. All the calculation steps are saved as a MATLAB Workspace (.mat) file in the same folder