You might try some brine treatments soaking him in a moderate salt solution for about 1/2 hour once a day. If he has raw open wounds start of with very weak salt solution like about a tablespoon per gal of water. These treatments should be done in a seperate container, not in his tank. The fact that he is still eating is a good sign. If you feel his condition is severe, consult a veterinarian. Skin problems in captive turtles are usually the result of poor water quality and or diet. You said you have a cannister filter but is it doing the job? Turtles are extremely hardy and given proper conditions and food they generally have very few health problems.

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