Start: 2022-08-26

Last update: 2022-08-29

1. Measure cell wrinkling

Add 200 x 200 grid to the picture, and measure the cell membrane length within a random square containing four grids (Fig. 2).

Aftet measuring 10 pictures, I found out that the variation within one picture is way too large. Depending on position of the cell, the readout can be longer when the cell just has a right-angle to the grid edge, or it can be shorter sometimes. This will mask the “real” differences in cell wrinkledness.

Add 100 x 100 grid to the picture, and measure the cell membrane length within a random grid (Fig. 3).

Note that two lines must lie on the opposite sides of the square. Including adjecent sides will increase the variations

Matlab Script

cd D:\Collaboration\Leora\PH2_24_untreated_ecoli\
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
I_4 = imread('PH2_24_untreated_15-20k-10df.jpg');
I_4 = im2gray(I_4)
imshow(I_4);

[rows, columns, numberOfColorChannels] = size(I_4);
hold on;
stepSize = 100;
for row = 1 : stepSize : rows
    line([1, columns], [row, row], 'Color', 'r', 'LineWidth', 1);
end
for col = 1 : stepSize : columns
    line([col, col], [1, rows], 'Color', 'r', 'LineWidth', 1);
end

title('Original Image', 'FontSize', fontSize);
axis on;
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off')
uiwait(msgbox('Left click, then right click'));
[x, y, intensityProfile] = improfile();
% Plot crosses over where you clicked.
hold on;
plot(x, y, 'r-', 'LineWidth', 3);
% Plot line
plot([x(1), x(end)], [y(1), y(end)], 'r+', 'LineWidth', 3, 'MarkerSize', 20);
% Plot intensity profile in another plot.
subplot(2, 1, 2);
plot(intensityProfile, 'LineWidth', 3);
grid on;
title('Intensity Profile', 'FontSize', fontSize);
distance = sqrt((x(1) - x(end))^2 + (y(1) - y(end))^2)
message = sprintf('The distance = %.1f pixels.', distance);
uiwait(helpdlg(message));