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A time series of Heterodera schachtii infecting MAGIC population of Arabidopsis thaliana.

Organisms: Arabidopsis thaliana

Standard RGB and multi-spectral images generated from VideometerLab4 for three wheat NDM lines' seeds

Organisms: Triticum aestivum

This collection includes 3D FIB-SEM datasets of Phaeodactylum tricornutum (strain 1 and strain 18) with segmentation labels for chloroplast and vacuole. It provides pretrained deep learning models developed across multiple architectures (3D VNet, 3D SegNet, 3D CNN 4-level, MONAI DynUNet, MONAI BasicUNet, Swin-Net + VNet hybrid, and Contrast-Aware Dual Encoder VNet). The dataset supports organelle segmentation research and transfer learning.

Imaging Methods: focussed ion beam scanning electron microscopy (FIB-SEM)

Source image data for figures 1-6 and appendix figures S1-S9

Imaging Methods: fluorescence microscopy

Organisms: Homo sapiens

This project contains four complementary datasets supporting Zhang et al. (2025). Dataset 1: Common Stocks (Welch Lab). Dataset 2: Shimkets Lab pretraining dataset. Dataset 3: Shimkets LS3934 nitrate experiments. Dataset 4: WT replicate dataset for aggregation fate analysis. Together these datasets cover the training, validation, and application phases of our deep learning framework for phenotypic quantification.

Organisms: Myxococcus xanthus

Human induced pluripotent stem cells (hiPSCs) are an attractive cell source for regenerative medicine. For its widespread use as a starting material, a robust storage and distribution system in the frozen state is necessary. For this system, managing transient warming during storage and transport is essential, but how transient warming affects cells and the mechanisms involved are not yet fully understood. This study examined the in uence of temperature cyclings (from−80°C to−150°C) on cryopreserved hiPSCs using a custom-made cryo Raman microscope, ow cytometry, and performance indices to assess viability. Raman spectroscopy indicated the disappearance of mitochondrial cytochrome signals after thawing. A reduction in the mitochondrial membrane potential was detected using ow cytometry. The performance indices indicated a decrease in attachment ef ciency with an increase in the number of temperature cycles. This decrease was observed in the temperature cycle range above the glass transition temperature of the cryoprotectant. Raman observations captured an increase in the signal intensity of intracellular dimethyl sulfoxide (DMSO) during temperature cycles. Based on these results, we proposed a schematic illustration for cellular responses to temperature uctuations, suggesting that temperature uctuations above the glass- transition temperature trigger the movement of DMSO, leading to cytochrome c oxidation, mitochondrial damage, and caspase-mediated cell death. This enhances our understanding of the key events during cryopreservation and informs the development of quality control strategies for hiPSC storage and transport.

Imaging Methods: recorded image

Organisms: Homo sapiens

External genital RGB images of conscious female ICR mice were recorded under normal fluorescent room lighting and annotated with estrous stage labels determined by vaginal smear cytology; these data were used to train and evaluate convolutional neural network models for non-invasive estrous staging.

Organisms: Mus musculus

Chromosome mis-segregation during meiosis in oocytes causes miscarriages and congenital diseases. Aging-associated premature chromosome separation is a major cause of mis-segregation. Effective prevention of premature chromosome separation has not yet been achieved. Here, we design protein-based artificial kinetochores that act as decoys to prevent premature chromosome separation. Designed artificial kinetochore-like decoys are submicroscale clusters of NDC80-NUF2-tethered protein particles that can establish a biorientation-like state by competing with chromosomal kinetochores for HURP-decorated microtubules. This competition reduces excessive bipolar microtubule pulling forces exerted on chromosomes, thereby effectively preventing premature chromosome separation during meiosis I and II in aged mouse oocytes. These effects suppress egg aneuploidy. This study provides a decoy strategy with biocompatible artificial kinetochores to prevent aging-associated meiotic errors in oocytes.

Imaging Methods: recorded image

Organisms: Mus musculus

The term polymethine dye (PMD) has been intimately linked to the dinuclear scaffold–two heterocycles linked together by a polymethine chain of varying length. Dinuclear PMDs have been a successful scaffold for non-invasive in vivo imaging in the biologically advantageous near infrared (NIR) and shortwave infrared (SWIR) regions of the electromagnetic spectrum. Trinuclear polymethine dyes, resulting from the addition of a third heterocycle into the polymethine chain, possess the same photophysical properties that make dinuclear dyes excellent fluorescent probes, but have yet to be investigated for in vivo imaging. Herein, we expand upon the dinuclear and trinuclear heptamethine scaffold by taking advantage of the increased reactivity of a cyclopentenyl linker and synthesize flavylium- and chromenylium-based SWIR-emitting fluorophores. The trinuclear scaffold instills the fluorophores with increased steric bulk, leading to beneficial photophysical properties in micelles and outperforming their classic dinuclear counterparts. In this work, we apply trinuclear PMDs for in vivo SWIR imaging in mice and find them to be particularly efficient at lymph node labeling upon intravenous administration.

Organisms: Mus musculus

Pheochromocytomas and paragangliomas (PPGLs) exhibit substantial molecular and immune heterogeneity, complicating risk assessment and treatment. Here, we define three distinct transcriptional subtypes (C1, C2, C3) through integrative transcriptomic and immunogenomic profiling. C1 is characterized by hypoxia-driven pathways and an immunosuppressive microenvironment, correlating with poor prognosis. C2 exhibits a highly inflamed immune landscape with robust CD8+ T cell infiltration, suggesting potential sensitivity to immunotherapy. C3 is enriched in metabolic reprogramming pathways and displays intermediate clinical outcomes. Genetic analysis reveals subtype-specific mutational patterns, with pseudohypoxic driver mutations (SDHB, VHL, SDHA, SDHD) predominant in C1 and C3, while kinase pathway alterations (NF1, RET) define C2. Single-nucleus RNA sequencing further delineates immune ecosystem diversity. Notably, we identify ANGPT2, PCSK1N, and GPX3 as key subtype-specific biomarkers, with ANGPT2 driving tumor progression in C1 and emerging as a potential therapeutic target. Our findings provide a refined molecular classification integrating immune and genomic features, offering a framework for improved prognostication and precision therapies in PPGLs.

Imaging Methods: bright-field microscopy

Organisms: Mus musculus

Programmed Cell Death Pathways Coordinate Neutrophil and Macrophage Clearance in Zebrafish and Are Differentially Exploited by Salmonella Typhimurium

Imaging Methods: fluorescence microscopy

Organisms: Danio rerio

Lung cancer is the leading cause of cancer-related deaths worldwide. Existing therapeutic options have limited efficacy, particularly for lung squamous cell carcinoma (LUSC), underscoring the critical need for the identification of new therapeutic targets. We previously demonstrated that the Transmembrane Serine Protease TMPRSS11B promotes transformation of human bronchial epithelial cells and enhances lactate export from LUSC cells. To determine the impact of TMPRSS11B activity on the host immune system and the tumor microenvironment (TME), we evaluated the effect of Tmprss11b depletion in a syngeneic mouse model. Tmprss11b depletion significantly reduced tumor burden in immunocompetent mice and triggered an infiltration of immune cells. RNA FISH analysis and spatial transcriptomics in the autochthonous Rosa26-Sox2-Ires-GfpLSL/LSL; Nkx2-1fl/fl; Lkb1fl/fl (SNL) model revealed an enrichment of Tmprss11b expression in LUSC tumors, specifically in Krt13+ hillock-like cells. Ultra-pH sensitive nanoparticle imaging and metabolite analysis identified regions of acidification, elevated lactate, and enrichment of immunosuppressive (M2-like) macrophages in LUSC tumors. These results demonstrate that TMPRSS11B promotes an acidified and immunosuppressive TME and nominate this enzyme as a therapeutic target in LUSC.

Imaging Methods: bright-field microscopy fluorescence microscopy

Organisms: Mus musculus