The Autonomous Benthic Explorer (ABE) is a vehicle designed to perform long-term autonomous repeatable surveys of the deep ocean. In this paper we examine the basic methodology of obtaining quantitative stereo measurements with ABE. We utilize stereo imagery collected during an autonomous survey along a tectonically active segment of the Juan de Fuca Ridge. The ability to make repeatable measurements is crucial for being able to carry out tasks associated with the detection of spatio-temporal changes. As this is one of the stated goals of ABE we have been developing a stereo camera system to make quantitative measurements from underwater imagery. Pursuant to our goals of long term deployments and the low power levels that such a goal imposes on each vehicle subsystem, our efforts have been focussed on the design of a low-energy stereo camera system. In this paper we describe our system and the methodology for its alignment and calibration in the typical harsh operating conditions associated with working on research platforms at sea. We demonstrate photogrammetric measurements at very fine scales of actual pillow lavas near a diffuse hydrothermal vent. We use a calibrated object to independently ground truth our results. Finally, we discuss improvements to these techniques which we intend to pursue.