###StackAlign

StackAlign is a Matlab toolbox for manually aligning images in a stack. It's primarily purpose in life is to align a small number (tens) of low-resolution images taken with a standard, fluorescence microscope.

StackAlign also has some basic image processing and analysis capabilities:

• Thresholding (e.g. for locating regions of fluorescence)
• ROI selection
• 3D displays of ROIs and thresholded images

Applications: *

StackAlign is work-in-progress.

###Documentation See example.m for a demonstration how to use the library.

####Filename conventions StackAlign always works in the current directory. Use the cd() command to change directory before running any of the StackAlign functions.

It is assumed that all image files in the current directory belong to the same image stack, and that they have the following filename structure:

Speciment_Region_Slide_Section_Stain.tiff

Example: CX34_BS_1_08_Nissl.tiff

####Toolbox functions saLoadStack Load images in current directory saConvertToUINT16 Convert all images to UINT16 saSortStack Sort stack by slide and section number saRegisterStack Register images in stack (translation, rotation) saMedianFilterImg Median filter images saDistributeTransform Distribute transformation parameters saDistributeTransform
saROIDraw
saGetThresholds