A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography

Advances, challenges, and applications of cryo-electron tomography workflows for three-dimensional cellular imaging of infectious pathogens

Cryo-electron tomography (cryo-ET) has become a powerful tool for visualising cellular structures at sub-nanometer resolution in their near-native state, offering unique insights into the molecular architecture of diverse biological systems, including infectious agents and their interactions with host cells. This paper reviews key methodologies and recent advancements in cryo-ET, with a particular focus on sample preparation of protozoan parasites and host cells. Topics covered include photopatterning for cell positioning on EM grids, vitrification techniques, whole-cell imaging, and cryo-FIB milling followed by cryo-ET. The manuscript also addresses how these approaches are providing valuable structural information on pathogens and pathogen-host interactions, which are critical for understanding mechanisms of pathogenesis and the development of therapeutic strategies. Additionally, we examine the principles and practical considerations of the multistep workflow, highlighting innovations such as integrated fluorescence microscopy (iFLM) within cryo-FIB SEM systems for improved target identification and lamella positioning. Challenges such as ion beam damage, sample thickness constraints, and the need for greater workflow automation are also discussed as areas for future improvement. As cryo-ET continues to evolve and deliver transformative insights into the molecular architecture of life, it inspires great hope for the development of future therapies against infectious diseases. LAY DESCRIPTION: Cryo-electron tomography (cryo-ET) is a special type of microscopy that allows researchers to look at the inside of cells in 3D, almost as if a hologram of the cell in its natural state was generated. This technique reveals molecular structures inside cells, allowing scientists to better understand how molecules and cellular components work together. To obtain such detailed images, biological samples need to be thin and frozen very quickly so that they remain undamaged and close to their natural state. One recent breakthrough involves using a tool called cryo-focused ion beam scanning electron microscopy (cryo-FIB SEM), which allows a thin slice of a frozen sample to be collected and then analysed using cryo-ET. In addition, photopatterning of support surfaces are being used to place cells in a strategic position for cryo-FIB SEM, and improved plunge freezing and high-pressure freezing methods have been developed to better preserve samples. Together, these techniques make it easier to reproducibly prepare high-quality samples for cryo-ET. These innovations allow capturing clearer and detailed images of cells, tissues, and even entire small organisms. Cryo-ET has led to important discoveries in biology, such as how proteins and other molecules interact within cells at the sub-nanometre scale. This technique holds great promise for revealing how life works at a molecular level, understanding diseases, and discovering new drugs.

Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues

Cryo-electron tomography (cryo-ET) has become a key technique for obtaining structures of macromolecular complexes in their native environment, assessing their local organization and describing the molecular sociology of the cell. While microorganisms and adherent mammalian cells are common targets for tomography studies, appropriate sample preparation and data acquisition strategies for larger cellular assemblies such as tissues, organoids or small model organisms have only recently become sufficiently practical to allow for in-depth structural characterization of such samples in situ. These advances include tailored lift-out approaches using focused ion beam (FIB) milling, and improved data acquisition schemes. Consequently, cryo-ET of FIB lamellae from large volume samples can complement ultrastructural analysis with another level of information: molecular anatomy. This review highlights the recent developments towards molecular anatomy studies using cryo-ET, and briefly outlines what can be expected in the near future.

Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives

Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.

Integrating cellular electron microscopy with multimodal data to explore biology across space and time

Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.