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Per default, octomap only cares about the geometric information, not the additional field like intensity or rgb data that is contained in some point clouds. There is functionality in Octomap for also using color information (see here for instance), but I think what you'll want is either prefiltering the cloud and throw out intensities you don't in your octomap, or using the Octomap API and update the octomap manually with more control over how the update is performed.