Li, W. et al. Proc. Natl. Acad. Sci. USA 114, E7321–E7330 (2017).

The function of a tissue depends on the distribution, identity and state of different cells that form the tissue. Analyzing the cellular organization in 3D can therefore help researchers understand complex tissues. Li et al. combined clearing-enhanced 3D microscopy with histocytometry to analyze tissue composition in mouse lymph nodes and other tissues. The researchers developed an optimized tissue-clearing protocol that maintained fluorescence from reporter proteins, that was compatible with immunolabeling and that retained cellular morphology. When combining their tissue-clearing approach with image analysis algorithms and cytometry tools, the researchers could quantify the distribution of B and T cells, macrophages and other cell types in mouse lymph nodes. As the clearing protocol is applicable to other tissues, the general strategy could be used to quantify cellular organization in other tissues as well.