Click here to download my simple LUTmaker software for creating ImageJ format color look-up tables (only available for the Windows operating system). Color lookup tables (LUTs) are used to display different image brightnesses, for example to view an X-ray of the arm, you might want to use a simple grayscale that shows air as black, bone as white and soft tissue as a gray. Alternatively, you can often detect more subtle differences by using a lookup table that shows differing intensities using both brightness and color changes. This software allows you to create LUT files in ImageJ format. This format describes 256 brightness values, with each intensity mapped using 8-bytes each of red, green and blue data. This format uses 768 bytes of disk space, with the first 256 bytes storing red data, followed by 256 bytes storing the green indexes and ending with the 256 blue indexes. The resulting lookup tables can be used with
NIH Image,ImageJ,XMedCon,MRIcro and
MRIcron.
My software allows you to easily create LUTs, but the LUTs it creates are contstrained (the darkest index is always black and the brightest is always white, with typically smooth transitions in between). If you want more flexibility (at the expense of ease) you should try some of the plugins available for Image that can create LUTs.
My software uses
Christophe Schlick's Fast Alternatives to Perlin's Bias and Gain Functions
to allow you to independently control the levels of red, green and blue in your LUT. It interactively displays the levels of these three colors as well as displaying the resulting LUT applied to a MRI scan. The left set of sliders adjusts the bias, while the right set adjusts the gain. Once you are happy with the resulting LUT, you can press the 'Save' button to create a *.lut file. To use a LUT with MRIcro, place the *.lut in the same folder as mricro.exe. To use a LUT with MRIcron, copy the file to the 'LUT' folder that exists in the same directory as MRIcron. When you restart these programs, they will automatically detect the look up tables. My program offers two ways to combine the bias and gain settings - you can apply them independently (as shown in the main figure), or you can click the 'Mix Gain/Bias' checkbox to make these values interact. Mixing is more intuitive, but you will never get local decreases in intensity (e.g. compare the blue line in the main figure to the mixed value on the right) which can create interesting lookup tables.
In 2012 I added another button labelled "LUT to CLUT" that converts any ImageJ format LUT (including the ones you create with LUTmaker) to MRIcroGL's CLUT format.
My mat2lut script converts a Matlab color matrix to an Osirix text-format LUT that MRIcron and MRIcro can read.
For example, the matrix "lut = [0.2 0 0; 0.5 0.5 0; 1 1 1];" will start have the lowest intensity be red
(20% red, 0% blue and 0% green), while it will appear violet in the middle range (50% red and 50% blue),
while the brightest voxels will appear white. Other than the "lut" matrix, the only thing you need to change is the
"filename" and "filenamelinear" parameters that select where the output files will be saved on your disk.
