16bit TIFF images generated by ImageJ appear black in MATLAB

Hi,

I have a database of 16bit TIFF images generated in ImageJ that I need to process in MATLAB. Apparently ImageJ is doing something to the image which makes it look almost completely black outside the framework of ImageJ (including MATLAB or any conventional viewer).

Moreover, if I open these TIFF images in ImageJ and then save them as JPEG, it suddenly opens normally outside the framework of ImageJ. But this doesn't solve the problem since JPEG loses information and since it is not practical to implement for a large amount of images.

Here you can find a sample TIFF & JPEG pair: TIFF: http://imgur.com/Arj5mzY JPEG: http://imgur.com/cpuXTni

EDIT: please use these links. they do not change the format of the image: TIFF: http://www.filedropper.com/tiff_1 JPEG: http://www.filedropper.com/jpeg

You can see that the TIFF image looks almost completely black, but if you open both the TIFF and the JPEG in ImageJ, they look the same.

What I need is the MATLAB code that converts the TIFF image generated by ImageJ, to a "real" TIFF that can be processed by MATLAB without changing\losing any information.

[Walter Roberson]

The first of those two links leads to a .png not to a .tif

Please attach the images directly here. You can zip them up and attach the zip if need be.

[Omer Yuval]

It let's you download it only as .png but it is originally a .tiff. I tried to upload it here directly but they do not support .tiff files. I'll try another way now.

[Omer Yuval]

TIFF: http://www.filedropper.com/tiff_1 JPEG: http://www.filedropper.com/jpeg

[Gopichandh Danala]

The 16-bit tiff file has all the information in it. The only problem is with the display range which makes them look like black but in fact, they have values around (200-350), whereas the brightest white pixels you see are having a very high value of around 16000. so the display range for your image is [133 16165]. so the small intensity pixels cannot be seen on the 16-bit tiff file but they are actually there.

In the case of the jpeg image, it is a uint8 bit and the display range is [22 255], which makes everything look clear.

[Gopichandh Danala]

If you are just worried about looking at them clearly change the display range

    figure, imshow(image,[0 1000])

by doing this all pixels which have a value over 1000 will be displayed as a white making everything in the range [0 1000] more clear to see

[Walter Roberson]

Note: files types that are not directly supported can be uploaded here by zip'ing them to create a .zip as .zip is supported.

[Walter Roberson]

If you use

info = imfinfo('TIFF.tif');

and examine info.ImageDescription then that contains

    'ImageJ=1.49e
     min=0.0
     max=1636.0
     '

this hints that 1636 is perhaps the expected maximum.

Answer 1

[Omer Yuval]

It worked!

Thanks a lot Walter Roberson.

The full general solution:

% use imfinfo('filename.tif') and strfind to find the minimum (m) and maximum (M) pixel values defined by ImageJ.

Im(find(Im < m)) = m;

Im(find(Im > M)) = M;

Im = (double(Im)-m) / M;

Or, if you just want to display the image:

imshow(Im,[m,M]);

[Image Analyst]

What if you simply use mat2gray():

lm = mat2gray(lm);

[Omer Yuval]

Nope...