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What and which versions are you using to generate the file? octomap and octovis released in ROS don't have color support yet (based on OctoMap 1.2).

If you use OctoMap trunk (the upcoming 1.4 version) there is now improved file support and color information. However, .cot files are not officially supported. You can convert them to the ".ot" file format with the "convert_octree" binary. octovis in trunk will then display the file correctly (you might have to enter the correct resolution manually in the file header because .cot did not store it).

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