However, as we can see in the header, this is still an 8-bit image, not a color (RGB) image. The result of the above manipulation, a2-color 8-bit image (red and green channels), with the red channel selected It is important to note that these are not RGB images, but 8 or 16 bit black and white images merged together, each with their own lookup table.įor example, consider the following two black and white images, membrane-GFP on the left and nuclear-mCherry on the right, from the same field In ImageJ, we can combine multiple black and white images into a pseudocolor image. Good further discussion of this issue can be found here and here Multi-color images and lookup tables You should always use a perceptual lookup table when applying this type of gradient color mapping. These can give rise to figures in which boundaries that do not exist are shown as an artifact of the color map. While the perceptual map applied to the bottom image again seems to smoothly transition between purple on the left and yellow on the right, our eyes pick out apparent discontinuities on non-perceptual jet color map above (for example, in the middle transition between yellow and orange). The same gradient of intensity values as above, encoded by the “mpl-viridis” lookup table The image above is identical to the one below, except for the fact that instead of intensities being mapped from black to white with varying shades of grey in between, they are mapped from black to green, with varying shades of green in between. Below is the same image with the “Grays” lookup table above and the “greens” lookup table below. In fact, all of the black and white images we’ve seen so far have already had a lookup table applied, the “Grays” lookup table, which is the default in imageJ. The final image is simply a 1:1 match between the grey values of the and the corresponding color values in the lookup table. A lookup table is a table where each possible grey value is assigned a corresponding RGB value representing a particular color. In imageJ, we can apply a lookup table (or LUT) to an image through the Image->Lookup Tables menu. However, if we do want to show the image in color, or if we want to overlay multiple colors into a multi-channel image, we need to map the grayscale image to a color map. When only one fluorophore is being imaged, it is in most cases best to leave the image in black and white. In fluorescence imaging, the primary data is always always one or more black and white images. The RGB intensity values for the pixel at (12,4) in the above image, as reported by ImageJ.
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