How to make a 3D Volume out of a 2D Tiff stack?

Question

Megan Clapperton 2018-6-1

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/403570-how-to-make-a-3d-volume-out-of-a-2d-tiff-stack

回答： yanqi liu 2021-11-22

I have a data set of 242 planes with x,y pixel resolution. It was taken from a microscope, I know the depth between image planes, and am looking to turn this Tiff Stack (split into individual files due to low RAM, named Flydata0000 - Flydata0242) into a 3D volume which I can eventually get a gui to play about with the image.

I have been trying Imshow to show an image array from reading the full file (containing only the fly data).

I will include what I have done already below (note I have not tried to make it 3D yet, would like corrections on what Ive done (if any) and an idea of how to go about making the stack 3D).

clearvars;
%Setting up path
fileFolder = 'E:\MyFile\Data\Low_Res\Sequence';
filePattern = fullfile(fileFolder, '*.tif');
TiffFiles = dir(filePattern);
% not using this now (fileNames = TiffFiles.name;)
numFrames = numel(TiffFiles);
for k=1:242
 fileNames = TiffFiles.name;
 fullfilename=fullfile(fileFolder, fileNames);
 fprintf(1, 'Now reading %s\n', fullfilename);
 imageArray = imread(fullfilename);
 imshow(imageArray);
 drawnow;
      %Alternate??
       % Stack=imread(['VeryLowResFly0' num2str(k, '%03.f') '.tif']);
       %Stack(:,:,k)=Stack;
       %imshow(Stack)
end

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Michael Nothem 2018-8-6

Did you get it figured out? I am trying to do the same thing!

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Answer 1

Rafael S.T. Vieira 2020-6-1

3
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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/403570-how-to-make-a-3d-volume-out-of-a-2d-tiff-stack#answer_443955

编辑：Rafael S.T. Vieira 2020-8-6

在 MATLAB Online 中打开

We need to create a 3D array WxHxD for storing all images, such as stack = zeros(W,H,D). Then, in the for-loop, we should read each image: stack(:,:,k) = imread(TiffFiles(k).name). For instance:

fileFolder = 'E:\MyFile\Data\Low_Res\Sequence';
filePattern = fullfile(fileFolder, '*.tif');
all_tiff  = dir(filePattern);
first_image = imread(all_tiff(1).name);
[W,H] = size(first_image);
D = numel(all_tiff);
stack = zeros(W,H,D);
stack(:,:,1) = first_image;
for i = 2:D
    stack(:,:,i) = imread(all_tiff(i).name);
    % uncomment next line for seeing the reading progress
    % disp(string(i*100.0/D) + "%");
end
% The app volumeViewer will handle the visualization
volumeViewer(stack);