Posted by
Unruh, Jay on
Nov 21, 2008; 6:22pm
URL: http://imagej.273.s1.nabble.com/doesn-t-recognize-ratio-command-tp3694424p3694431.html
John,
I'm not entirely sure what you mean, but Figures 5 and 3 of that paper do not contain any pixel intensity information. From my knowledge of Enrico's program, these Images were first threshholded and then false colored according to their GP values with threshholded values showing up as black. You could make something like this in ImageJ by first masking your GP image with a threshholded intensity image the then false coloring the resulting image with a LUT that shows low intensity values as black. Unfortunately, if you have 0.0 GP values, they will also show up as black. Alternatively, you could create the intensity threshhold mask, then create the false color RGB image, split it into R, G, and B images using RGB split, then mask each of these images and finally recombine them using RGB merge. There may be an RGB mask plugin out there that would do this without the split/merge steps.
Jay Unruh
Stowers Institute for Medical Research
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of John Oreopoulos
Sent: Friday, November 21, 2008 11:54 AM
To:
[hidden email]
Subject: Biased/stretched LUTs in ImageJ
Hi,
I have a calculated image formed by the ratiometic combination of two other images. I want to preserve the resulting pixel intensities in the calculated image which is 32-bit. I have several calculated images like these and their pixel intensities vary widely. I'd like to display these images with a colored look up table but be able to stretch LUT to bias the contrast to certain values for each image in a similar manner to what was done in Figure 3 and Figure 5 of the following paper:
Parasassi, T., E. Gratton, W.M. Yu, P. Wilson, and M. Levi, 1997. Two- photon fluorescence microscopy of Laurdan generalized polarization domains in model and natural membranes. Biophysical Journal 72:
2413-2429.
When I take my calculated images and add a colored calibration bar for the LUT, I can adjust the brightness and contrast to get the desired effect, but the pixel intensities no longer match the original calculated image. Is there a way to do this properly in ImageJ without altering my pixel intensities?
John Oreopoulos