Nature Methods, Published online: 24 April 2024; doi:10.1038/s41592-024-02242-5Super-resolution imaging of reference and target structures enables precise determination of the labeling efficiency of high-affinity binding proteins in cells for improved quantitative assessment of protein organization at the single-molecule level.

Nature Methods, Published online: 24 April 2024; doi:10.1038/s41592-024-02255-0SABR-IIs are engineered bifunctional receptors that enable CD4+ T cell antigen discovery.

Nature Methods, Published online: 23 April 2024; doi:10.1038/s41592-024-02263-0To those who seek transcriptomic information at high resolution, scale and throughput, single-cell RNA sequencing brings the data. Scientists share tips and future plans as they reflect on the method’s rise to stardom.

Nature Methods, Published online: 23 April 2024; doi:10.1038/s41592-024-02240-7This Perspective discusses the potential of protein structure-prediction models for exploring the structural landscape and specificity of TCR–pMHC interactions.

Nature Methods, Published online: 22 April 2024; doi:10.1038/s41592-024-02246-1We created DELiVR, a deep-learning pipeline for 3D brain-cell mapping that is trained with virtual reality-generated reference annotations. It can be deployed via the user-friendly interface of the open-source software Fiji, which makes the analysis of large-scale 3D brain...

Nature Methods, Published online: 22 April 2024; doi:10.1038/s41592-024-02245-2Generating training data for training deep-learning-based tools is time consuming. The DELiVR pipeline facilitates this process as demonstrated in this study on detecting c-Fos+ cells or microglia in the brain, following tissue clearing and imaging with light-sheet microscopy.