Saving Cell Contents to Images in Loop for ImageJ

Hi,

I have a 4D data set A(m,n,j,k). In a for loop the data is "squeezed" into a cell A_cell to make k 3D cell entries each A_cell{k} = A(m,n,j). Each cell entry is saved as a .mat in the home directory within the loop.

Now in the loop(or not), I need to open either each cell or each saved .mat file, generate j tif images for each of the cell/.mat entries/files, and then save these images as tiff with numbered names back into the home directory.

I am using this function to generate ImageJ-readable images from the 4D data sets.

Can somebody please help with this?

Thanks!

Answer 1

[Image Analyst]

Should be very easy with this http://matlab.wikia.com/wiki/FAQ#What_is_a_cell_array.3F and this http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F. Inside the loop, create an outputfilename with sprintf() and fullfile (like the FAQ shows) and then get the image from the cell array with braces

thisImage = myCellArray{index};

Then call imwrite

baseFileName = sprintf('..........
fullFileName = fullfile(folder, baseFileName);
imwrite(thisImage, fullFileName);

[Avigdor]

Thanks! This looks a lot like the code I've assembled now to get to the point where I've divided the 4D matrix A(m,n,j,k) I started from into the cell array consisting k 3D matrices A_cell{k}=A(m,n,j). Now, I suppose saving a .mat files or images is similar in the loop, but how can I save images from each 3D cell as j indexed images A(m,n)? I'm a little stuck at the loop structure. Also, using imwrite, how does this function know which images to export?

[Image Analyst]

Something like

folder = pwd; % Or whatever you want.
for k = 1 : size(A, 4)
    % Extract kth frame (a color image) from the 4D image.
    thisImage = A(:,:,:,k);
    % Create filename.
    baseFileName = sprintf('Frame %d', k);
    fullFileName = fullfile(folder, baseFileName);
    % Write to disk.
    imwrite(thisImage, fullFileName);
end

I don't see why it's necessary to mess around with cells if you already have a 4D matrix.

[Avigdor]

Thanks again for the tips. It's not quite what I am trying to do. I am having trouble reducing the dimensionality of the matrices, and incorporating this in the output file loop. Ideally the images will be saved with index, Image_k_i. In this example there are k=11 images, each with i=16 image sequences, 1_2,1_3...11_1,11_...11_16. Total k*i 256x256 images. Here's an example of what I have:

% 4D mat file data4D=A(256,256,16,11);

for k = 1:size(data,4)   
for i=1:size(data,3)
% reduce from 4D to 3D
data3D=squeeze(abs(data4D(:,:,1:1:end,k)));

$reduce from 3D to 2D
data2D=squeeze(data3D(:,:,i));

% save k*i 2D mat files to tiff baseFileName = sprintf('Frame %d.tif',i); fullFileName = fullfile(dir,baseFileName); imwrite(mat2gray(data2D), fullFileName); end end

[Avigdor]

Got it. Needed a second index in the baseFileName. Did not realize you could do that.

baseFileName = sprintf('Frame %d.tif',k,i);

Thanks!

[Image Analyst]

But that's not right , as I'm sure you figured out. You should have (in most cases) the same number of %d as you do variables. For example, this:

k=10;
i = 2;
baseFileName = sprintf('Frame %d.tif',k,i)

gives:

baseFileName =
Frame 10.tifFrame 2.tif

which is NOT a good filename. If you have a number k, and a number i, what do you want the filename to look like.

[Avigdor]

Hi. This saves the images well, but the name is messy I agree. I'm looking for a filename like Frame 1_Step_1.tif to Frame_k_Step_i. For each frame k there are i steps. Also, do you have experience with the Tiff function? I'm trying to save the tiffs as 32-bit as the ImageJ function is having problems with the 16-bit output. Thanks for the follow-ups!

[Avigdor]

For the naming I've tried this and it's better:

file_name = strcat('Frame_', num2str(k),'Step_', num2str(i),'.tif');

How about the 32-bit image saving?

[Image Analyst]

I would use sprintf but include the Step part:

file_name = sprintf('Frame_%d, Step_%d.tif', k, i);

It looks simpler to me and more like other languages you're familiar with like C and Java.

[Avigdor]

Thanks! I posted a question about saving 32-bit tiff images in this context. Please check it out if you have some insight.

http://www.mathworks.com/matlabcentral/answers/163626-saving-indexed-tif-images-from-for-loop-problem-with-file-size