[image, map] = imread('filename.tif') returns empty color map? Image file is a 32-bit z-stack.

Hi: I'm trying to read a 98-slice 32-bit z-stack into MATLAB. It is the result of a distance transformation with a LUT applied. As you can see, if I call imfinfo, it shows that each slice has a color map. So why is it that when I call for example, [z1, map] = imread('filename.tif', 1) I get an empty ([]) map? Also, if I am using the Tiff class to write my result again, as a single 32-bit float type .tif file, is there a way I can save the LUT as well? I have attached one slice of the z-stack if anyone wants to take a closer look. Thanks!

Answer 1

[Image Analyst]

I don't understand why a floating point image would have a colormap stored with it. How can the floating point number be used as a row index into your 256 element colormap? How did you generate "ans", your structure. Was it by calling imfinfo() with the same filename as using imread(), so they're both reading the very same file? Can you attach that file? Have you tried using the Tiff class instead of imread() to read in the images?

[Max Lu]

Hi: Thanks for the reply. Yes, imfinfo() is called on the same file as in imread(). It is a 98 slice z-stack obtained from a distance transform done on a two-photon z-stack sample of the same size, processed with Imaris (the LUT is applied in Imaris). When I click on the cell that shows the 256 element color map here is what it looks like (256 x 3 double). Also if you want to see a slice of the z-stack, here is it what it looks like in ImageJ (2nd figure). I've also attached the slice as a zip file if you want to take a look. Thanks!

[Image Analyst]

What does this say

whos z1

Put that after you use imread() to get z1.

[Max Lu]

z1 (name) 369x381 (size) 562356 (bytes) single (class)

[Image Analyst]

You might need to use the 'index' keyword:

[z1, map] = imread('filename.tif', 'index', 1);
whos map
if isempty(map)
  warndlg('Map is empty');
else
  helpdlg('Map has stuff in it');
end

I think might come down to a colormap not making sense for a floating point image. Why do you think one is applicable?

You might have to talk to tech support and send them your image for them to figure out if it's resolvable or not. Otherwise save your image as uint8 if you want a colormap. Or else just don't worry about the colormap.

[Max Lu]

Hey, thanks for the suggestions, I will see if I can talk to tech support. In my case, the image is floating point because the intensity values actually represent distances (so 1.1002 is really 1.1002 microns for example) and a LUT helps to visually represent regions of greater distance vs. regions of proximity by coding the distance values with colors.