Run Z_projection_and_contrast_enhancement.py on raw stack.tiff files (calls functions defined in Z_proj_functions.py). This script averages all slices in the stack, and outputs the projected images as .tiff with normalised and stretched intensity to increase contrast, and a .csv table containing each image, path, name, ID, and theoretical displacement values.
This step strongly relies on correct file naming (ID_x_value_y_value_z_value) and file order, and could be modified to allow for user error.
Run Sort_and_align_skimage_cross_correlation.py on the projected files obtained from 1. (calls functions defined in Registration_cross_correlation.py). This script applies a cross correlation function to align the images, and outputs a summary image for each set of 3 images (initial (0;0), translation (tx,ty), and return to (0;0)) depicting the aligned images, and the estimated displacement compared to the initial (0;0) in µm and pixels. It also saves a .csv table of these values.
Run Cross_correlation_graphs.py to obtain summary plots showing the error in X and Y translation, as well as the error in returning to zero after a known translation.
Files should be used as follow :