This repository contains two MATLAB programs used to extract information from Airyscan images of S. Pombe cells.
These codes requires two colored Z-stack Airyscan images containing 40 z-slices each, along with the two ROI manager files obtained by using ImageJ. An ROI manger file contain node or contractiel ring (CR)
ROIs to extract intensities and the other contain background ROIs to subtract background.
 
A) NodeBroadband.m 
Automatically extract node intensity and total broad band intensity after subtracting their background. It also calculates cell size parameters such as cell, length, width, surface area and volume. 
It works with one cell at a time in an image and extracts information from a broad band of nodes. It requires following two ROI-manager files as mentioned above.

Node_RoiSet.zip: Contain x-y-z positions of nodes and the last ROI is a polynomial area of the broad band of nodes.
NodeBroad band_background ROI: Contain in the order x-y-z positions of 8 circles from each tip and ROIs of cell length, cell width and cell boundaries from SUM projected image.

Demo image file 'NodeBroadband.czi', corresponding node coordinate file 'Node_RoiSet.zip' and background file 'background_RoiSet.zip' are also provided in the folder. The program compile results in the form
of an excel file in the same folder containing image file.

B) CRAnalysis.m
Automatically extract CR intensity after background subtraction. It also calculates cell size parameters such as cell, length, width, surface area and volume. 
It can extract information from more than one CR in differet cells from the same image. 
it also requies two zip 'ROI manager' files from ImageJ.

CR_RoiSet.zip: CR_RoiSet.zip: Contain outline ROI of contractile ring, cell length, cell diameter and outline of the cell in the order. 
CR_backgroundRoiSet.zip: Contain, in the order first two ROIs from two tips of the cell showing CR. If second cell is also present with the CR in the same image then 3rd and fourth ROIs are from the two cell tips of the second cell and so on.
 
Demo image file 'CR.czi', corresponding 'CR_RoiSet.zip' and 'CR_backgroundRoiSet.zip' files are also provided in the folder. The program compile results in the form of an excel file in the same folder containing image file.

Please see the following manuscript for detailed analysis
 https://www.biorxiv.org/content/10.1101/2021.07.02.450929v1