We describe a He-Xe comagnetometer operating in stemless anodically bonded cells with a 6 mm volume and a Xe spin coherence time of 300 sec. We use a Rb pulse-train magnetometer with co-linear pump and probe beams to study the nuclear spin frequency shifts caused by spin polarization of He. By systematically varying the cell geometry in a batch cell fabrication process we can separately measure the cell shape dependent and independent frequency shifts. We find that a certain aspect ratio of the cylindrical cell can cancel the effects of He magnetization that limit the stability of vapor-cell comagnetometers. Using this control we also observe for the first time a scalar He-Xe collisional frequency shift characterized by an enhancement factor $\kappa_{} = -0.011\pm0.001$.

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