Reviews & Analysis

We introduce TransBrain, a computational framework for bidirectional translation of whole-brain phenotypes between humans and mice. TransBrain enables quantitative cross-species comparison in a unified latent space and facilitates functional modeling of the human brain in mouse models.

This Review provides a comprehensive discussion of how methods in machine learning and computer vision have been used to improve super-resolution microscopy to gain insights into subcellular biology.

We developed SmartEM, a method that integrates machine learning directly into the image acquisition process of an electron microscope. By allocating imaging time in a specific manner — scanning quickly at first, then rescanning only critical areas more slowly — we are able to accelerate the mapping of neural circuits up to sevenfold without sacrificing accuracy.

This Perspective envisions the future of 3DTFM and provides practical guidelines for experimental and computation strategies for its application.

DynamicAtlas is a new open-source tool for incorporating gene expression and tissue shape changes into a single atlas with a continuous developmental timeline.

A technique called SASS increases temporal signal-to-noise ratio for functional MRI by taking advantage of the time it takes to reach steady state when collecting functional images.

We developed SpaceBar, a method that uses DNA barcodes to label both individual cells and their progeny and seamlessly integrates with high-resolution imaging-based spatial transcriptomics technologies. This new approach enables the elucidation of how a cell’s location and ancestry jointly inform its function and gene expression in complex tissues.

We present MultiCell, a geometric deep-learning model capable of predicting multiple types of cell behaviors over time during the dynamic process of embryonic development. MultiCell sets the stage for data-driven quantitative modeling of multicellular developmental dynamics at single-cell precision.

This Review introduces ten cell migration assays, offers practical guidance toward selecting the best assay for a specific biological question and describes how future advances can reveal important insights into dynamic cellular behaviors.

This Review describes the principles of data analysis for extracting quantitative data from cell migration assays. It also highlights advanced image analysis tools and offers practical guidance for interested users.

The gold standard system for mRNA imaging in live cells just got upgraded by being degraded. This development improves signal-to-noise ratios and may lead to a better understanding of mRNA transport and localization.

We systematically mapped how morphogen timing and dosage shape early cell fate specification in human neural organoids to unify our understanding of neural regionalization and to accelerate development of organoid models. This defined competence windows for key signaling pathways and benchmarked variability across human pluripotent stem cell lines and protocols.

The Carta algorithm infers a differentiation map — including progenitor cell types and transitions between progenitor and terminal cell types — from high-throughput lineage tracing data. Applying Carta to mouse hematopoiesis and embryoid developmental datasets reveals new intermediate progenitors and a secondary origin for a specialized cell type.

This Perspective reviews computational methods for cross-species knowledge transfer and introduces ‘agnology’, a data-driven concept of functional equivalence independent of evolutionary origin.

TIRTL-seq is an innovative method that allows efficient and cost-effective identification of αβ TCR clones from millions of T cells with the aid of a pairing algorithm called T-SHELL, which provides high accuracy and throughput in sequencing paired TCR clones.

Nondestructively mapping biological tissues in 3D with nanoscale detail is essential to scale up the study of how cells interact in their environment, such as in neuronal circuits. We resolved such ultrastructure in brain tissue using coherent X-ray phase-contrast imaging techniques, which extends the volume imaging toolbox with nondestructive approaches.

The plant cell wall makes the preparation of high-quality cells for single-cell RNA sequencing challenging. To tackle this issue, we developed FX-Cell, a method that enables the enzymatic digestion of the cell wall at high temperatures to result in high-quality single plant cells for transcriptome analysis.

We introduce the Cryo-EM Image Evaluation Foundation (Cryo-IEF) model, which has been pretrained on 65 million particle images in an unsupervised manner. Cryo-IEF excels in diverse cryogenic electron microscopy data-processing tasks; it automates the complex workflow and makes this technology more accessible and robust.

This Perspective overviews recent and emerging developments in building and using multimodal foundation models based on transformers for analyzing various types of genomics data.

Engineered acoustic reporter genes with differential responses to the pressure of sound waves enable multiplexed ultrasound imaging and visualization of different cell types deep inside optically opaque living tissues.