This demo includes some easy examples of the Spectral Imaging Toolbox.
If anything is unclear in these examples refer to the User Manual pdf 
included in the Spectral Imaging Toolbox folder for a quick-start, non-technical guide.

Watershed-based segmentation:

For the watershed-based segmentation example, choose "objects and membranes" as the segmentation mode.
Check the two-term Gaussian fitting checkbox.
Leave the GP correction factor fields blank.
Specify 439 and 493 as the low and high wavelengths. 
Specify "Watershed-based segmentation example" as the input and output folder.
In the Object Separator: 
Remove the segmented objects that are not cells by navigating using the arrows
on the keyboard to those images and clicking "remove current image".
Set the current image to the one containing two touching cells. 
Enter 3 as the number of objects in the input box.
Click "automatically separate" and review the segmentation attempt.
"Accept" changes then "submit".
"Submit" in the Membrane Segmentation GUI.
Review the results in the output folder.

Lasso segmentation:

For the lasso segmentation example, choose "objects and membranes" as the segmentation mode.
Check the two-term Gaussian fitting checkbox.
Leave the GP correction factor fields blank.
Specify 439 and 493 as the low and high wavelengths. 
Specify "Lasso segmentation example" as the input and output folder.
In the Object Separator: 
Remove the segmented objects that are not cells by navigating using the arrows
on the keyboard to those images and clicking "remove current image".
Set the current image to the one containing two elongated and touching cells. 
Click "manually separate".
Draw a region around one of the cells without including pixels from the other cell.
After reviewing the segmentation attempt, "accept" changes then "submit".
"Submit" in the Membrane Segmentation GUI.
Review the results in the output folder.

Spherical object mode:

For the spherical object mode example, choose "spherical objects" as the segmentation mode.
Leave the GP correction factor fields blank.
Choose 439 and 493 as the low and high wavelengths. 
Specify "Spherical object mode example" as the input and output folder.
In the Circle Finder GUI: 
Choose the lower and upper bounds. 10 and 55 works reasonably well for this image.
Click "submit for this image".
In the Membrane Segmentation GUI:
Use the arrows on the keyboard to navigate through the segmented images. 
"Remove current image" where the segmentation is not satisfactory.
Click "submit" and review the results in the output folder.
Note that the size distribution histogram is not useful for such a low number of objects. 
This feature is useful, however, when running the Spectral Imaging Toolbox in spherical object mode 
on a folder containing many images.

Z-stack reconstruction example:

For the z-stack reconstruction example, choose "no segmentation" as the segmentation mode.
Leave the GP correction factor fields blank.
Choose 563 and 654 as the low and high wavelengths. 
Specify "Z-stack reconstruction example" as the input and output folder.
Click "submit" and review the results in the output folder.
The 3D GP map will be located in the results folder under "No segmentation/GP/8-3D reconstruction.fig".
