imread altering image in Matlab?

Question

I am having an issue reading a single image of a stacked tiff in using imread. The tiff is 128-by-126. It reads in just fine with ImageJ, but I try reading it into Matlab for some processing and it creates an odd streak in the center of the image. With the origin of the image in the top left, rows 63 and 64 are repeated as rows 65 and 66, and the last two rows of the image, 125 and 126 are cut off. I can tell this is happening by visual comparison of the image displayed in matlab to the image displayed in ImageJ.

If I take the same tiff stack, and save the first frame in ImageJ, I don't have this issue. Even when displaying the outputted matlab image using ImageJ, I see the same issue. However, I would like to automate the process to save images from several tiff stacks as single tiff files, which I can't do in ImageJ, so I turned to Matlab and ran into this issue. I have included my code below. I tried reading the tiff in two different ways and got the same error. It seems to be related to the tiff stack and how matlab reads in the tiffs. I am using Matlab R2012b.

I have included links below to the static ImageJ image I am seeing and the static matlab image I am seeing. I have also included a link for loading the stacked tiff file that is generating these issues for me.

Note: When I have ImageJ output each frame as an individual tiff and I open the first frame from that output in matlab using the same code below, the image is correctly displayed. The error only occurs when reading in the first frame from the image stack in Matlab.

StackOverflow doesn't support embedding TIFF files, but you can view and download them from these links:

• Stacked Tiff File - Data I am working with

• What the first frame should look like - ImageJ

• What I am seeing when loading the first frame in MATLAB

Code Used to Generate the Image

fname='C:\FileLocation\pcd144_012.tif';
im1=imread(fname,1)
imagesc(im1);
axis image; colormap gray;

I tried reading in the image as a tiff object to see if it solved the problem and this didn't work either. The image has two strips, and the last two lines of the first strip are the same as the first two lines of the last strip, which is why the middle lines seem to be repeated. It seems matlab is indexing reading my image in wrong, likely because it is not a square image. Am I just doing something wrong, or does matlab have a bug with respect to reading in non-square tiffs? Any ideas or suggestions for improvement?

Answer 1

First of, I kinda agree with horchler, that is, there is something wrong in your header.

We can easily observe that the StripByteCounts (15872) does not match width*height (128*126). This could be the reason you see the repetition in row 63 - 64 and 65 - 66.

Since the RowPerStrip = 64 and StripOffsets = [8,15880] may indicate that you have a 128*124 graph, Matlab perhaps uses last two rows in the first 64 rows to pad the missing rows at the beginning of the rest of the rows. So the total row can be filled up to 126. Well, this is just my guess for how Matlab handles the disagreement between dimension and ByteCounts.

After all, to your question, imread indeed alters image in Matlab when reading TIFF without issuing any warning. Bad job in imread reading TIFF, Matlab.

After observing your TIFF frames in one of your links, the TIFF seems to actually have image data with dimension 128*126. So if you trust the dimension indicating in the header, you would probably use fread to read the frames in your TIFF instead of using shaky imfread.

fname='pcd144_012.tif';
tiffInfo = imfinfo(fname);
framIndex = 1;
tiffWidth = tiffInfo(framIndex).Width; % image width
tiffHeight = tiffInfo(framIndex).Height; % image height
tiffStartOffset = tiffInfo(framIndex).StripOffsets(1); % Image data offset start point
tiffEndOffset = tiffInfo(framIndex).StripOffsets(2); % Image data offset end point
fid = fopen(fname);
fseek(fid,tiffStartOffset,'bof');
im1 = fread(fid,tiffWidth*tiffHeight,'*uint16'); % We knew this from BitsPerSample 
fclose(fid);
im1 = reshape(im1,tiffWidth,tiffHeight); % Reshape the image data array
figure
imagesc(im1);
colormap gray;
axis xy;
axis image; 

Now, while this may solve the weird Matlab imread behavior, however, the above result still does not match the picture you showed in your second link. According to the picture in the second link, it has 300 frames but the one you attached in your first link only has 30 frames. Maybe we are all looking at the wrong picture?