MATLAB: Difference visualizing image ImageJ (Bio-Format) and Matlab

Image Processing Toolboximagej

I have a problem visualizing a stack/multipage tiff file with both ImageJ (Bio-Format plug-in) and MATLAB. In the MATLAB file there seems to be more noise or higher background values compared to the ImageJ image. This is not in the visualization, but the ratio between signal (circles) and background differs between the two images. However, I cannot find if there is something wrong with my MATLAB script in visualizing the images. As I thought it can simply be done with imread (see code below).
Image = '0000127_01_800.TIF';
info = imfinfo('0000127_01_800.TIF');
num_images = numel(info);
for k = 1:num_images
A = imread(Image,k,'Info', info);
B{k} = A
Does someone has experience with both ImageJ and MATLAB who can maybe help me to understand this difference?

Best Answer

Your file is a multipage tiff file (with what looks like 3 levels of magnification of the same image). When you use matlab to open the file, you load the raw pixel data, which renders as you've seen.
On the other hand, the bio-format plugin that you use in ImageJ knows how to use that raw pixel data and the associated metadata (which you can see in matlab by using imfinfo) to convert these raw pixels into the image you see in ImageJ. Without knowing what that process is, it's difficult to reproduce the image in matlab.
However, it would appear that Bio-Formats can also be used directly in matlab. So, follow the instruction and use the plugin in matlab.