Cells are the basic unit of human organs that are not fully understood. The revolutionary advancements of optical imaging allowed us to observe single cells in whole organs, revealing the complicated composition of cells with spatial information. Therefore, in this review, we revisit the principles of optical contrast related to those biomolecules and the optical techniques that transform optical contrast into detectable optical signals. Then, we describe optical imaging to achieve three-dimensional spatial discrimination for biological tissues. Due to the milky appearance of tissues, the spatial information blurred deep in the whole organ. Fortunately, strategies developed in the last decade could circumvent this issue and lead us into a new era of investigation of the cells with their original spatial information.Cells are the basic unit of human organs that are not fully understood. The revolutionary advancements of optical imaging allowed us to observe single cells in whole organs, revealing the complicated composition of cells with spatial information. Therefore, in this review, we revisit the principles of optical contrast related to those biomolecules and the optical techniques that transform optical contrast into detectable optical signals. Then, we describe optical imaging to achieve three-dimensional spatial discrimination for biological tissues. Due to the milky appearance of tissues, the spatial information blurred deep in the whole organ. Fortunately, strategies developed in the last decade could circumvent this issue and lead us into a new era of investigation of the cells with their original spatial information.

全脑介观神经联接研究是解析脑认知功能的神经输入输出环路结构基础、普查基因表达与细胞类型，以及绘制全景立体脑图谱的科学前沿。光学成像方法在横向方向能够达到亚微米的分辨率，并可通过多种手段实现“光学切片”的效果，具备在介观水平观测神经环路的天然优势。基于组织透明或机械切削的自动化全脑显微光学成像方法，突破了光学成像在生物组织中成像深度的限制，具有在大范围内提供介观水平精细观察的技术优势。结合各类生物样本荧光标记技术，全脑显微光学成像方法在神经环路的结构和功能的研究方面有着巨大潜力，已成为剖析全脑神经及血管网络的最佳方式。为了更全面地了解和认识这种有力的工具，总结了近年来发展的各类全脑显微光学成像方法，并展望了未来的技术发展。

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.

荧光分子层析(FMT)成像是一种具有深度分辨能力的宏观光学成像技术，可定位和量化生物体内的荧光分子探针，在蛋白质相互作用研究、药物作用机制解析以及肿瘤治疗效果评价等方面具有巨大的应用潜力。然而，FMT的一个关键挑战是其逆向问题具有高度病态性，这意味着图像重建对测量噪声及各种数值误差非常敏感。要获得良好的图像重建结果，除了尽可能提升系统的性能以减小测量噪声外，还主要取决于两个方面：一是提高正向问题求解的精度以降低数值误差；二是缓解逆向问题的病态性使其抗噪声能力更强。本综述介绍了目前FMT图像重建在这两个方面的研究进展。

双光子荧光显微成像是一种非线性光学显微技术，具有高空间分辨率、高信噪比和固有的三维层析分辨能力等优点。传统的双光子荧光显微成像通常使用波长可调谐的100 fs超短脉冲激光器作为激光光源。目前，人们对双光子荧光显微成像方法进行了深入研究，改进光源及探测方法是常用的手段。介绍和总结了多色双光子荧光显微成像技术的近期研究进展及其在生物医学中的应用。首先介绍了传统飞秒激光器及光学参量振荡器在多色成像中的应用，然后对光纤超连续谱在多色显微成像中的应用进行了分析，最后简要说明了增强自相位调制效应产生连续光谱以及选择性激发实现多色成像的工作。多色双光子成像技术不仅可以同时获取含有多种荧光团的待测样品的高对比度双光子荧光图像，而且具有系统结构简单、操作简便等优点，这使得其在生物医学和材料科学等领域具有广阔的应用前景，并且为生物医学诊断与研究提供了一种有效的工具和平台。

Hypoxia is closely related to many diseases and often leads to death. Early detection and identification of the hypoxia causes may help to promptly determine the right rescue plan and reduce the mortality. We proposed a new multiparametric monitoring method employing mitochondrial reduced nicotinamide adenine dinucleotide (NADH) fluorescence, regional reflectance, regional cerebral blood flow (CBF), electrocardiography (ECG), and respiration under six kinds of acute hypoxia in four categories to investigate a correlation between the parameter variances and the hypoxia causes. The variation patterns of the parameters were discussed, and the combination of NADH and CBF may contribute to the identification of the causes of hypoxia.

The 5th Russian_Chinese Workshop on Biophotonics and Biomedical Optics was hosted in Saratov, Russia on 26_28, September, 2012. The bilateral Workshop brought together both Russian and Chinese scientists, engineers and clinical researchers from a variety of disciplines engaged in applying optical science, photonics and imaging technologies to problems in biology and medicine. During the Workshop, 2 plenary lectures, 11 invited presentations, 4 oral presentations and 13 poster reports were presented. A special Internet session with 5 presentations—1 plenary, 2 invited, and 2 posters, was also organized. This special issue selects some papers from the attendees, and is made up of 12 original research articles and one review. Seven articles have been presented in Vol. 6, No. 1 of JIOHS; this issue presents the remaining six articles.