A method and apparatus for counting seedlings. A seedling moves through a seedling counter, which comprises a spectral energy emitter and a spectral energy detector. When the spectral energy detector detects a sufficient attenuation of the spectral energy for a sufficient amount of time, the spectral energy detector indicates the presence of a seedling. The spectral energy detector detects irregularities in the received spectral energy to indicate faults in the apparatus. In one embodiment, the seedling counter is adapted to use X-ray energy.