How can I see in red the pixels over a certain value and blue under another value

I am not sure if this can be done with the threshold tool or by creating a LUT or in another way.
In a greyscale image I want to mark with red the pixels over a “high threshold” and blue the pixels under a “low threshold”. In between, we can keep the original image or it can be seen as white.

If possible, something that can be implemented in a macro.
Thank you!!

Another option is to use the HiLo LUT (Image > Lookup Tables > HiLo; available in #fiji, see also the Visualization page on the wiki).

(This solution differs from the one suggested by @anon96376101 mainly in that it changes the display of the intensities between the low and high “thresholds” to be in the full range between black and white.)

  • Open any 8-bit grayscale image (e.g. the Gel sample image).

  • Switch to the HiLo lookup table (Image > Lookup Tables > HiLo).

  • Adjust the Minimum and Maximum to your desired values in the B&C window (Image > Adjust > Brightness /Contrast… or Shift+C); you can also use the Set button to enter the values in a dialog in a recordable way.

  • If you want to use this image outside ImageJ (e.g. in a presentation or figure), convert it to RGB (Image > Type > RGB Color).

I leave it as an exercise to you to record this as a macro using the recorder.

2 Likes

Thank you very much Herbie and imagejan, I appreciate your help.

The HiLo method works well, and Herbie’s macro works well in imageJ 1.52a, but for some reason does not work properly in Fiji: it only keeps the upper (red) threshold, not the blue one, and I get an Exception window. I will try to run it step by step to find out the reason.

Regards

My macro was tested under the curent daily build of ImageJ which is version 1.52k71. Please up-date your Fiji to the same version.

I just tried version 1.52j and it gives me a

java.lang.NullPointerException
at ij.plugin.frame.RoiManager.moveRoisToOverlay(RoiManager.java:2332)

but provides the desired result.

Consequently, please work with the daily build.

Regards

Herbie