Guided ablation instruments are disclosed for creating lesions in tissue, especially cardiac tissue for treatment of arrhythmias, including atrial fibrillation. In one aspect of the invention, a percutaneous catheter is disclosed with an endoscope positionable in the instrument's distal end region to obtain an image. The image allows the clinician to determine whether contact has been achieved (or blood has been cleared from an ablative energy transmission path) before ablation begins or while ablation is occurring. In one embodiment, percutaneous ablation catheters are disclosed having at least one central lumen and one or more balloon structures at the distal end region of the instrument. Also disposed in the distal end region are an illuminating light source and an endoscope capable of collecting sufficient light to relay an image to the user. The instruments can further include an ablation element. The ablation element can be a contact ablation element, or a radiant energy emitter, which is preferably independently positionable within the lumen of the instrument and adapted to project ablative energy through a transmissive region of the instrument body (and/or balloon) to a target tissue site proximate to the pulmonary veins. The energy can delivered without the need for contact between the energy emitter and the target tissue so long as a clear transmission pathway is established. The endoscope element of the instrument allows the clinician to determine the position of the instrument and, if radiant energy is to be employed, see if such a pathway is clear. Moreover, because the position of the radiant energy emitter can be varied, endoscopic guidance permits the clinician to select a desired location and dose for the lesion.
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