How to convert the colored tif picture into grayscale with corrosponding intensity?

luts
color-analysis
measure
Tags: #<Tag:0x00007fd5408a70d8> #<Tag:0x00007fd5408a6f98> #<Tag:0x00007fd5408a6e58>

#1

Hi everyone.
I have obtained some 8-bit color images by EPMA. In these pictures, different colors indicated different intensities, (there is a histogram to indicate the intensities). I want to convert these colored pictures into grayscale with intensities corrospondingly, and then combine these grayscaled images together using channel merge , and then add different colors to each channel to compare differences of their distribution and intensity. Do you have some suggestion? thank you very much.
by the way, I have already changed these colored pictures into grayscale by Edit > Options > Conversions > (checked)scale with conversion, weighted RGB conversions, Image > type > 8-bit. But the conversion results are not in accordance with intensities indicated by the histogram, especially the red spots. See details in the attached pictures.


Original file: tif

Original file: tif
Thank you very much!

Amy


#2

Good day Amy,

please realize what 8bit color means!
Please study:
https://imagej.nih.gov/ij/docs/guide/146-9.html#sub:Pseudocolor-Images

8bit color images are no RGB images, hence conversion by changing them to gray-value cannot work by simply changing the image type!

As you’ve indicated, you need to know the applied LUT. A known LUT can be converted. In your case the LUT is very coarse, i.e. the steps are big and converting it will perhaps be not very satisfying: A lot of the original information (of the gray-valued image before applying false color) may be lost.

Regards

Herbie


#3

Amy,

here is what I get when converting the false color image to gray according to the given LUT:

The gray steps ideally are 13.5 and the top two steps are the same. The values at the scale bar are about the fourfold gray values.

Regards

Herbie


#4

Hi Herbie,

Thank you very much, it really helps.
Did you use some Macro, Or just convert this by the existed Image J plugin?

Amy


#5

Good day Amy,

your problem needs an individual solution.

If you’ve read the short section about false color and perhaps a bit more about LUTs, you should realize that you need a custom LUT that gets you from the color LUT to a reasonable gray LUT.

After having studied the manual, you should be able to convert the present color LUT to a reasonable gray LUT. The tools are provided by ImageJ. Getting a useful LUT for the conversion may take a while (of thinking and doing) …

i’d begin by looking at the present color LUT:

  1. Open your image in ImageJ
  2. “Image > Color > Show LUT”
  3. In the then opening dialog click on “List…”
  4. Save the LUT-list as text file

Then I’d modify a copy of the color LUT:

  1. Save a copy of the LUT-list and open it in a text editor
  2. In the text editor, modify the copy to contain reasonable gray values
  3. Gray values have the same value for Red, Green and Blue

Have success

Herbie


#6

Hi Herbie,

Thank you very much for your reply in such a detailed manner (that is what i need, i am new on ImageJ ). this a good solution.
And I have found another solution, there is a macro written by @oburri, it also helps a lot.
Thanks!

Best regards!
Amy


#7

Great that this works for you! Would you mind linking to the macro or post, so that others reading this topic will be able to follow?

Thanks.


#8

Hi, imagejan,
Of course I can post the link here. But I think this has already been post in ImageJ forum by @oburri. Shall I post it here again?


#9

Alright, I found it now. The forum allows to cross-embed posts marking the text of interest and then pressing the Quote button that appears. So here is the link to the other forum topic:


#10

Thank you very much.
But I am not good at this.

Best!