More diversity at the top: A detailed knowledge of cell differentiation hierarchies is important for understanding diverse biological processes such as organ development, tissue regeneration, and cancer. Single-cell RNA sequencing can help elucidate these hierarchies, but it requires reliable computational methods for predicting cell lineage trajectories. Gulati et al. developed CytoTRACE, a computational framework based on the simple observation that transcriptional diversity—the number of genes expressed in a cell—decreases during differentiation. CytoTRACE outperformed other methods in several test cases and was successfully applied to study cellular hierarchies in healthy and tumor tissue. Science , this issue p. 405

We present a tiling light sheet microscope compatible with all tissue clearing methods for rapid multicolor 3D imaging of cleared tissues with micron-scale (4 × 4 × 10 μm3) to submicron-scale (0.3 × 0.3 × 1 μm3) spatial resolution. The resolving ability is improved to sub-100 nm (70 × 70 × 200 nm3) via tissue expansion. The microscope uses tiling light sheets to achieve higher spatial resolution and better optical sectioning ability than conventional light sheet microscopes. The illumination light is phase modulated to adjust the position and intensity profile of the light sheet based on the desired spatial resolution and imaging speed and to keep the microscope aligned. The ability of the microscope to align via phase modulation alone also ensures its accuracy for multicolor 3D imaging and makes the microscope reliable and easy to operate. Here we describe the working principle and design of the microscope. We demonstrate its utility by imaging various cleared tissues.

Double duty for mammary stem cell niche: The stem cell niche is a complex local signaling microenvironment that regulates stem cell activity for tissue and organ maintenance and regeneration. As well as responding locally, during puberty, the mammary gland stem cell niche also responds to systemic hormonal signals. Zhao et al. have found that Gli2, a transcriptional effector of Hedgehog signaling, coordinates the niche-signaling program and activates expression of receptors for the mammatrophic hormones estrogen and growth hormone throughout the mammary gland (see the Perspective by Robertson). Disease may result not only from stem cell defects, but also from dysregulation of the microenvironment. Science , this issue p. eaal3485 ; see also p. 250