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The authors established a volumetric trans-scale imaging system with an ultra-large field-of-view (FOV) that enables simultaneous observation of millions of cellular dynamics in centimeter-wide three-dimensional (3D) tissues and embryos. Using a custom-made giant lens system with a magnification of ×2 and a numerical aperture (NA) of 0.25, and a CMOS camera with more than 100 megapixels, they built a trans-scale scope AMATERAS-2, and realized fluorescence imaging with a transverse spatial resolution of approximately 1.1 µm across an FOV of approximately 1.5×1.0 cm2. The 3D resolving capability was realized through a combination of optical and computational sectioning techniques tailored for our low-power imaging system. They applied the imaging technique to 1.2 cm-wide section of mouse brain, and successfully observed various regions of the brain with sub-cellular resolution in a single FOV. They also performed time-lapse imaging of a 1-cm-wide vascular network during quail embryo development for over 24 hr, visualizing the movement of over 4.0×105 vascular endothelial cells and quantitatively analyzing their dynamics. Their results demonstrate the potential of this technique in accelerating production of comprehensive reference maps of all cells in organisms and tissues, which contributes to understanding developmental processes, brain functions, and pathogenesis of disease, as well as high-throughput quality check of tissues used for transplantation medicine.

Imaging Methods: recorded image fluorescence microscopy AMATERAS-2w AMATERAS-1 spinning disk confocal microscopy AMATERAS-2c

Organisms: Homo sapiens Mus musculus Coturnix japonica

Reprocessed images from LINCS image dataset and Human Protein Atlas for training deep learning models.

Imaging Methods: fluorescence microscopy confocal microscopy

Organisms: Homo sapiens

Understanding the factors involved in chromatin dynamics is crucial for the study of biochemical processes in which distant genomic regions need to come in close proximity. Previous single locus tracking studies suggest that chromatin dynamics are linked to active transcription, but studies which compare the chromatin dynamics of different locations within a defined chromatin domain are still very limited. Here we used the ANCHOR3 DNA labeling system to track multiple cis-regulatory elements and non-regulatory control regions at different positions in the mouse Klf4 locus. We observe homogeneous chromatin motion of cis-regulatory elements and non-cis-regulatory control regions in Klf4 transcribing mESCs and their non-transcribing EpiLCs daughter cells. These observations challenge the notion that active transcription has a major effect on the locus dynamics of mammalian genes.

Imaging Methods: spinning disk confocal microscopy

Organisms: Mus musculus

Multiscale 3D image datasets of mammalian placental tissue

Imaging Methods: electron microscopy X-ray microscopy

Organisms: Mus musculus

Figure 7 Raw Data

Organisms: Setaria viridis

Eukaryotic chromosome segregation requires attachment of chromosomes to microtubules through the kinetochore so that chromosomes can align and move in mitosis. Kinetochores assemble on the centromere which is epigenetically defined by the histone H3 variant CENtromere Protein A (CENP-A). During DNA replication CENP-A is equally divided between replicated chromatids and new CENP-A nucleosomes are re-assembled during the subsequent G1 phase. How cells regulate the cell cycle timing of CENP-A assembly is a central question in the epigenetic maintenance of centromeres. CENP-A nucleosome assembly requires the Mis18 complex (Mis18α, Mis18β, and M18BP1) which is regulated in its localization to centromeres between metaphase and G1. Here, we define a new regulatory mechanism that works through phosphorylation of Xenopus laevis M18BP1 between metaphase and interphase. This switch disrupts binding of M18BP1 to CENP-A nucleosomes in metaphase, and when relieved enables M18BP1 binding to CENP-A nucleosomes in interphase. We show that this phosphorylation dependent mechanism regulates CENP-A nucleosome assembly. We propose that the phospho-regulated binding of M18BP1 to CENP-A nucleosomes restricts new CENP-A assembly to interphase.

Imaging Methods: spinning disk confocal microscopy

Organisms: Xenopus laevis

Original images

Imaging Methods: bright-field microscopy confocal microscopy

Organisms: Platynereis dumerilii

Figure 6 Raw Data

Organisms: Setaria viridis

The subcellular localization of a protein is important for its function, and its mislocalization is linked to numerous diseases. Existing datasets capture limited pairs of proteins and cell lines, and existing protein localization prediction models either miss cell-type specificity or cannot generalize to unseen proteins. Here we present a method for Prediction of Unseen Proteinsí Subcellular localization (PUPS). PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images. We demonstrate that the protein sequence input enables generalization to unseen proteins, and the cellular image input captures single-cell variability, enabling cell-type-specific predictions. Experimental validation shows that PUPS can predict protein localization in newly performed experiments outside of the Human Protein Atlas used for training. Collectively, PUPS provides a framework for predicting differential protein localization across cell lines and single cells within a cell line, including changes in protein localization driven by mutations.

Imaging Methods: spinning disk confocal microscopy

Organisms: Homo sapiens

The mechanisms underlying early Parkinson’s disease (PD) remain unexplained. While the aggregation of alpha-synuclein (αSyn) into Lewy bodies (LBs) characterises the pathology of later stages, emerging evidence suggests that small, toxic αSyn oligomers may drive disease during the pre-symptomatic phase. Here, we introduce the concept of Aggregation-Susceptible Cells (ASCs): neurons that, due to elevated intracellular αSyn concentration, are predisposed to forming pathological aggregates. Using quantitative imaging, we identified 9,882 neurons containing 112 million αSyn oligomers across multiple brain regions from post-mortem human tissue of early-stage PD cases and controls. No increase in intracellular αSyn concentration in early disease was found; in other words, there is no “unique cell” in PD with an unexpectedly high αSyn oligomer concentration. However, the proportion of ASCs was significantly elevated in brain regions undergoing early pathological manifestation. This finding supports a model in which idiopathic PD pathogenesis is not driven by a change in αSyn aggregation kinetics at the protein level, but rather by an increased prevalence of neurons stochastically crossing a critical concentration threshold for aggregation at the cell-population level. These results identify cell aggregation susceptibility as a fundamental mechanism in the earliest transition to pathology and offer a new quantitative framework for understanding early-stage protein misfolding in PD.

Imaging Methods: spinning disk confocal microscopy

Organisms: Homo sapiens

Research utilising exercise therapeutically to enhance neuroplasticity mainly reports enhanced expression of neurotrophic (neural growth) factors which are associated with increased neurogenesis, structural changes, and improved memory. However, these neural changes are tightly regulated by both promotors and inhibitors of neuroplasticity, and the effect of exercise on inhibitory pathways is currently understudied. We show that exercise also modulates inhibitors of neuroplasticity. Six weeks of treadmill training reduced the gene expression of aggrecan, a chondroitin sulphate proteoglycan (CSPG), and altered the composition of CSPG containing structures, perineuronal nets, in the rodent hippocampus. Genetically manipulating chondroitin-4-sulphation of CSPGs by overexpressing hippocampal Chst11 impaired memory performance, which was mitigated by treadmill training. We provide evidence that hippocampal CSPGs are involved in object recognition memory, and that there is a link between exercise, modulating hippocampal inhibitors of neuroplasticity, and memory performance.

Imaging Methods: fluorescence microscopy

Organisms: Rattus norvegicus

This dataset comprises live-cell fluorescence resonance energy transfer (FRET) and corresponding bright-field images of MCF-7 cells co-expressing the fluorescently tagged proteins CFP-BCL-XL and YFP-BAK under various drug treatment conditions. The data were acquired using quantitative FRET microscopy to simultaneously capture dynamic drug-target interactions and morphological changes at single-cell resolution. This resource enables the quantitative analysis of drug-induced modulation of BCL-XL/BAK interactions, the correlation between target engagement and phenotypic outcomes, and the development of computational models for drug efficacy scoring. The dataset is an essential resource for researchers in cancer biology, drug discovery, and high-content image analysis, providing a foundation for studying dynamic protein-protein interactions and functional drug responses in a live-cell context.

Organisms: Homo sapiens