Search GIDE databases

This dataset contains multichannel fluorescence images from an adapted Cell Painting assay applied to 3D colorectal cancer spheroids. Spheroids were generated in ultra-low attachment microplates, cleared to improve optical transparency, and imaged across multiple channels to capture morphological variation throughout the spheroid volume. The image analysis pipeline includes automated spheroid detection, cell segmentation, and feature extraction, with outputs normalized across plates and imaging depths. It provides a resource for scalable, image-based profiling in physiologically relevant 3D spheroid models.

Imaging Methods: spinning disk confocal microscopy

Organisms: Homo sapiens

Purpose: Retinal ganglion cell (RGC) loss in glaucoma occurs in a large fraction of patients even after intraocular pressure (IOP) is reduced. Mitochondrial dysfunction is a key mechanism that links elevated IOP to RGC degeneration. We tested whether HDAP2, a novel high-density aromatic peptide that binds cardiolipin to stabilize mitochondrial membranes, can protect RGCs in the DBA/2J mouse model. Methods: DBA/2J mice received HDAP2 (3 mg/kg, intraperitoneally, every other day) starting at 4 months of age for 8 months. IOP was measured each month to track pressure exposure. RGC survival was assessed by counting RBPMS-stained cells in retinal wholemounts and optic nerve axons in semithin toludine blue-stained sections. Results: HDAP2-treated retinas had ~49% more RGCs than untreated retinas at similar pressure exposures (p = 0.0063; F(2,59) = 5.524). At mild IOP exposure, HDAP2 preserved 58% more RGCs compared with untreated retinas, and at high IOPs, RGC survival was 180% greater. Kaplan–Meier analysis indicated that HDAP2 increased the threshold for severe RGC loss by 29 mmHg and reduced the chance of developing severe RGC degeneration by a factor of 4.6. Optic nerve axons from treated retinas were also well preserved, with axon morphologies appearing indistinguishable from controls. Axon size distributions did not change significantly among the treatment groups, suggesting that protection by HDAP2 was similar among RGC subtypes. Conclusions: HDAP2 preserved both RGCs and axons in a pressure-dependent manner and increased tolerance to IOP. These results suggest that HDAP2 may complement pressure-lowering therapy, including for normal-tension and treatment-refractory glaucoma.

Imaging Methods: bright-field microscopy confocal microscopy

Organisms: Mus musculus

MERFISH of adult human skin across 114 samples, 22 donors, and 15 anatomic sites. H&E of adult human skin

Imaging Methods: bright-field microscopy microscopy

Organisms: Homo sapiens

Adipose tissue is a central organ for controlling systemic metabolism both in invertebrates and vertebrates. Here, we have investigated the developmental processes of the adult-type fat body (AFB) in Drosophila. We have established genetic tools that allow visualization and genetic manipulations of cells in the AFB lineage from early in metamorphosis. We identified precursor cells that give rise to the AFB and delineated dynamic cellular behaviors underlying AFB formation. These precursor cells displayed polarized cell shapes and oriented motility, with emigration from the thorax and subsequent dispersal to the abdomen and head. After the migration period, these cells adhered to each other, assembling into the AFB with a sheet-like architecture. Continuous cell proliferation occurred during and after the large-scale migration to achieve appropriate fat tissue mass. Homotypic cell fusion after the sheet formation contributed to the establishment of multinucleated cells in the AFB. We also examined candidate gene functions, and our results argue that ecdysone signaling and the transcription factor Serpent support adult fat body organogenesis.

Imaging Methods: time lapse microscopy recorded image

Organisms: Drosophila melanogaster

Original image data of the manuscript by Itakura et al.

Imaging Methods: recorded image

Organisms: Drosophila melanogaster

Loss of pluripotency is an essential step in postimplantation development that facilitates the emergence of somatic cell identities essential for gastrulation. Before implantation, pluripotent cell identity is governed by a gene regulatory network that includes the key transcription factors SOX2 and NANOG. However, it is unclear how the pluripotency gene regulatory network is dissolved to enable lineage restriction. Here we show that SOX2 is required for postimplantation pluripotent identity and cells that lose SOX2 expression in the posterior epiblast are no longer pluripotent. Using in vitro and in vivo analyses we demonstrate anticorrelated expression of Nanog and Sox2 preceding gastrulation, culminating in an early disappearance of pluripotent identity from posterior NANOGhigh/SOX2low epiblast. Surprisingly, Sox2 expression is repressed by NANOG and embryos with post-implantation deletion of Nanog maintain posterior SOX2 expression. Our results demonstrate that the distinctive features of post-implantation pluripotency are underpinned by altered functionality of pluripotency transcription factors, ensuring correct spatio-temporal loss of embryonic pluripotency.

Imaging Methods: confocal microscopy

Organisms: Mus musculus

Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes are physically limited by objective-to-specimen distance, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed a photochemical strategy for spatially precise sectioning of specimens. By combining serial photochemical sectioning with lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelin sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory-bulb-wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative brain, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach.

Imaging Methods: fluorescent label

Organisms: Mus musculus

The honeybee gut microbiota plays a key role in shaping host health and susceptibility to disease. Yet, the nutrient environment it experiences within the gut remains poorly characterized. In particular, little is known about the spatial distribution of nutrients across this community, as resolving such fine gradients in vivo has been technically challenging. Here, we engineer the native honeybee symbiont Snodgrassella alvi as a living biosensor to quantify the bioavailability of the dietary sugar arabinose within the gut. By expanding the genetic toolkit for S. alvi through chromosomal integration of high-burden genes and a suite of low-strength promoters, we achieve stable multi-gene expression without compromising host colonization. The resulting biosensor generates a specific, dose-dependent response to arabinose in situ, enabling visualization of sugar gradients across gut-associated bacterial biofilms at micron-scale resolution. Using this system, we show that diet-derived arabinose distribution is highly heterogeneous and can be influenced by the metabolic activity of co-colonizing Gilliamella species. These findings highlight how diet composition and microbial specialization generate fine-scale microenvironments within the gut. More broadly, this work further establishes S. alvi as a genetically tractable platform for in situ probing of microbial metabolism and nutrient distribution.

Imaging Methods: confocal microscopy

Organisms: Apis mellifera

All imaging regards the study evaluating the role of GBP1 in phagolysosomal response of macrophages to mycobacteria. Folders correspond to each specific figure.

Imaging Methods: confocal microscopy

Organisms: Homo sapiens

RTX toxins (Repeat in ToXins) are pore-forming toxins secreted by gram-negative bacteria. They are known for their ability to disrupt host cell membranes, among which various human cells. The acylation of specific lysine residues in these toxins is crucial for their hemolytic activity, but the precise mechanisms underlying this enhancement remain unclear. By comparing the lytic activities of acylated MbxA and its non-acylated form, we explored the role of acylation in the pore-forming behaviour of this RTX toxin. Our findings demonstrate that acylation specific interactions of MbxA with cholesterol promote membrane disruption, both in vitro and in living cells. More specifically, acylation is not necessary for initial membrane binding, but markedly enhances pore formation. Overall, our results provide detailed insights into the molecular determinants that regulate MbxA toxin activity. We highlight a complex interplay between lipid composition (sterols), acylation, and membrane disruption, thereby advancing our general understanding of RTX toxin pathogenesis.

Organisms: Homo sapiens

Video files (.avi) of 10-20 worms moving in a 2D arena without any stimulus. Each video is an independent replicate of a strain that's either wild-type or mutant for genes in the hedgehog pathway.

Imaging Methods: macroscopy

Organisms: Caenorhabditis elegans

Fluorescence imaging across the near-infrared (NIR, 700–1000 nm) and shortwave infrared (SWIR, 1000–2000 nm) regions offers significant advantages for biomedical applications, yet photophysical enhancements achieved with NIR and SWIR chromophores observed in solution often fail to translate to complex biological environments. Fluorous-soluble fluorophores, fluorofluorophores, face additional challenges, exhibiting poor brightness and photostability when dissolved in perfluorocarbons (PFCs) due to unfavorable interactions with the fluorous phase. Here, we report counterion exchange as a strategy to enhance the photophysical properties of two heptamethine cyanine fluorofluorophore for NIR and SWIR imaging. Exchanging the small chloride counterion with a large, fluorinated aryl borate counterions significantly improved the brightness (10-fold) and photostability (57-fold) in PFCs. These enhancements were successfully translated across multiple biological systems from macrophage cells to NIR imaging zebrafish retinal tissue and finally to SWIR imaging in mice. These results demonstrate that strategic counterion modification provides a straightforward approach to optimize fluorofluorophores, with solution-phase improvements that translate to in vivo NIR and SWIR imaging.

Organisms: Mus musculus