elgw / df_cc

widefield microscopy, chromatic aberrations

Correction for shift and low order chromatic aberrations

This repository contains code to correct for shifts and chromatic aberrations between wide field microscopy channels. The implementation is based on a paper by Michal Kozubek, although any bugs or misconceptions are likely to be mine.

Typically these functions are used on calibration beads to set up a mapping between a reference channel (pick the best one) and the other channels.

These files are slightly out of context here as they are part of a bigger toolbox (DOTTER) which also contains a GUI.

To use these files with MATLAB, it might be a good idea to add the corresponding folder to the path, i.e.

addpath('~/where/i/keep/df_cc/')

Note, there is no code to extract dots from images here, and for any practical usage, the input should be fitted coordinates. For exploring these functions, a good starting point might be df_cc_demo1.m.

Files

Create a correction (.cc) file:

• df_cc -- Cluster dots to find correspondences, and find correction. Uses the following functions:
• df_cc_cluster -- find correspondences between points.
• df_cc_create -- find the transformation between two or more channels.
• df_cc_view -- metrics about the correction results.

Note: the .cc files used to store data are just normal .mat files that can be loaded with the -mat switch to load.

Correct dots

• df_cc_apply_dots -- transform dots to match a reference channels

Correct images:

• df_cc_apply_image -- correct a single image
• df_cc_apply_image_folder -- correct all images in a folder

Demos/tests

• df_cc_demo1 -- demo using a constant shift / dot correction.
• df_cc_ut -- some unit tests

Utility files

These files are used by the other scripts:

• df_cc_eudist euclidean distance
• df_cc_poly2mat -- create matrix for finding coefficients.

Depreciated

• df_cc_apply_m -- Correct M.dots in a DOTTER .NM file.
• df_cc_apply_n -- Correct all N.userDots in a DOTTER .NM file.

TODO

• Use a polynomial also in the axial direction?
• Add some more demos and demo images.