Adaptive optics (AO) is a powerful tool for optical microscopy to counteract the effects of optical aberrations and improve the imaging performance in biological tissues. The diversity of sample characteristics entails the use of different AO schemes to measure the underlying aberrations. Here, we present an indirect wavefront sensing method leveraging a virtual imaging scheme and a structural-similarity-based shift measurement algorithm to enable aberration measurement using intrinsic structures even with temporally varying signals. We achieved high-resolution two-photon imaging in a variety of biological samples, including fixed biological tissues and living animals, after aberration correction. We present AO-incorporated subtractive imaging to show that our method can be readily integrated with resolution enhancement techniques to obtain higher resolution in biological tissues. The robustness of our method to signal variation is demonstrated by both simulations and aberration measurement on neurons exhibiting spontaneous activity in a living larval zebrafish.