Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous largescale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.Cancer forms and progresses through a series of critical transitions-from pre-malignant to malignant states, from locally contained to metastatic disease, and from treatment-responsive to treatment-resistant tumors (Figure 1). Although specifics differ across tumor types and patients, all transitions involve complex dynamic interactions between diverse pre-malignant, malignant, and non-malignant cells (e.g., stroma cells and immune cells), often organized in specific patterns within the tumor

We report on the synthesis of organized arrays of gold (Au) nanoparticles on thermally oxidized Si wafers using sputtering as a metal deposition method in combination with sphere lithography. This simple process leads to the formation of a honeycomb mask of Au at room temperature (RT). We study the transformation mechanism of this honeycomb mask to a hexagonal array of Au nanoparticles by annealing at different temperatures and in different atmospheres. The underlying mechanisms of pattern formation during annealing are coalescence of particles and Ostwald ripening and depend on temperature and atmosphere. The crystallinity and orientation of the nanoparticles with respect to the underlying substrate is analyzed by electron backscatter diffraction (EBSD), and the control of the morphology, size, shape, and orientation in different atmospheres (argon (Ar), nitrogen (N2), air, hydrogen (H2), and vacuum) is discussed.

We describe the design and performance of an orthogonal time-of-flight (TOF) secondary ion mass spectrometer that can be retrofitted to existing focused ion beam (FIB) instruments. In particular, a simple interface has been developed for FIB/SEM instruments from the manufacturer Tescan. Orthogonal extraction to the mass analyser obviates the need to pulse the primary ion beam and does not require the use of monoisotopic gallium to preserve mass resolution. The high-duty cycle and reasonable collection efficiency of the new instrument combined with the high spatial resolution of a gallium liquid metal ion source allow chemical observation of features smaller than 50 nm. We have also demonstrated the integration of a scanning probe microscope (SPM) operated as an atomic force microscope (AFM) within the FIB/SEM-SIMS chamber. This provides roughness information, and will also allow true three dimensional chemical images to be reconstructed from SIMS measurements.

In this paper a brief summary of results from characterization of microstructures in the coating layers of selected irradiated fuel particles with burnup of 11.3% and 19.3% FIMA will be given. The main objectives of the characterization were to study irradiation effects, fuel kernel porosity, layer debonding, layer degradation or corrosion, fission-product precipitation, grain sizes, and transport of fission products from the kernels across the TRISO layers. Characterization techniques such as scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, and wavelength dispersive spectroscopy were used. A new approach to microscopic quantification of fissionproduct precipitates is also briefly demonstrated. Microstructural characterization focused on fission-product precipitates in the SiC-IPyC interface, the SiC layer and the fuel-buffer interlayer. The results provide significant new insights into mechanisms of fission-product transport. Although Pd-rich precipitates were identified at the SiC-IPyC interlayer, no significant SiC-layer thinning was observed for the particles investigated. Characterization of these precipitates highlighted the difficulty of measuring low concentrations of Ag in precipitates with significantly higher concentrations of Pd and U. Different approaches to resolving this problem are discussed. An initial hypothesis is provided to explain fission-product precipitate compositions and locations. No SiC phase transformations were observed and no debonding of the SiC-IPyC interlayer as a result of irradiation was observed for the samples investigated. Lessons learned from the post-irradiation examination are described and future actions are recommended.

The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

Pop-ins, or sudden displacement-bursts at constant load in a nanoindentation test, are typically attributed to the difficulty of setting up potent dislocation sources in the very small indentation zones in these experiments. Such displacement (and strain) bursts would intuitively indicate a sharp drop in stress during the pop-in event itself. However, spherical indentation stress-strain curves routinely exhibit a high and stable indentation stress value during the pop-in, and the indentation stresses decrease only after a further finite amount of additional indentation displacement has been applied. In order to understand this discrepancy, we utilize a combination of interrupted spherical indentation tests along with depth profiling of the residual indentation surfaces using in-situ atomic force microscopy (AFM) to study pop-ins. The AFM surface profile maps show that there is an asymmetric profile change over a limited region around the indentation contact area for a single pop-in; the asymmetry disappears upon further loading beyond the pop-in. A plausible sequence of physical processes (related to metal plasticity) occurring underneath the indenter during and immediately after the occurrence of the pop-in is proposed to explain these observations.

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Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) and three-dimensional (3D) imaging, including both optical and scanning electron microscopy (SEM) methods, that allow pathologists and cancer biology researchers to identify areas of interest from human cancer biopsies. The protocols and mounting strategies described in this workflow are compatible with 2D large format EM 2 mapping, 3D focused ion beam-SEM and serial block face-SEM. The flexibility to use diverse imaging technologies available at most academic institutions makes this workflow useful and applicable for most life science samples. Volumetric analysis of the biopsies studied here revealed morphological, organizational and ultrastructural aspects of the tumor cells and surrounding environment that cannot be revealed by conventional 2D EM imaging. Our results indicate that although 2D EM is still an important tool in many areas of diagnostic pathology, 3D images of ultrastructural relationships between both normal and cancerous cells, in combination with their extracellular matrix, enables cancer researchers and pathologists to better understand the progression of the disease and identify potential therapeutic targets.