import numpy as np
import colorsys
from skimage import io

if __name__ == "__main__":
    image = np.zeros((1, 256, 3))
    for i in range(256):
        color = np.array(colorsys.hsv_to_rgb(i / 256, 1, 0.8))
        image[:, i, :] = np.tile(color, (1, 1))
    io.imsave('tmp.png', (image * 255).astype(np.uint8))

    # sample X colors:
    x = 16  # must be a square if an int, examples: 16, 25, 36 etc
    colors = np.array([colorsys.hsv_to_rgb(i, 1, 0.8) for i in np.linspace(0, 1, x + 1)][:-1])
    colors = colors.reshape((int(x**0.5), int(x**0.5), 3))
    io.imsave('samples.png', (colors * 255).astype(np.uint8))

tmp.png:

samples.png:

Still has rather similar greens but you get what I mean :-)

(yes the python code is inefficient. This is a proof of concept and not representative of the programmers abilities :-D )

The labels in my example are consecutive integers. And even if they weren't the color mapping should skip unused integer values. Use equivalent of np.unique(segmentation) to determine used labels and set the map accordingly.

This issue persists in snapshot 2021-10-01 and is a real dealbreaker. I don't agree with the low priority @kislinsk

I understand that multilabel is the way to go in the future but it suffers from exactly the same problem and having to change that manually for every label in for every segmentation is it very user-unfriendly. I like to use MITK to inspect segmentation results so I need to be able to view many different segmentations in quick succession. That is only possible if MITK provides good default colors.

The problem was mentioned again in the tested checklists:

I procrastinated on the colors tonight for quite some time and finally found something that really stood out - the standard distinguishable color palettes of R:

https://stackoverflow.com/questions/50321000/r-colors-many-distinctive-colors-that-are-still-pretty

Kelly is nice because it is not overly saturated as most other palettes, but I think the most useful is indeed glasbey, when the two black-ish and one grey-ish colors are removed for our context. Red and magenta both appears pretty similar twice. Also, the colors should be a reordered a little bit and for the sake of compatibility/expectations start with red. More or less the same for polychrome but there we would also need to get rid of more grey colors.

This is my shot at it mainly based on the palettes above with extra effort regarding neighboring color contrasts (top-left to bottom-right). But it is impossible to get 25 perfectly distinguishable colors. Also I took into account that the human eye has the highest sensitivity in the green spectrum.