Cellular & Molecular Imaging

Individual 3D cell shapes of Drosophila Wing Disc

This record contains the raw and reconstructed imaging data (imaris) underlying the cortical organoid experiments in Sheu et al., "Coupled transcriptomic divergence establishes a human-specific synaptic glial precursor state." Cortical organoids derived from human, chimpanzee, and gorilla pluripotent stem cells were fixed at two culture timepoints (DIV60 and DIV160) and immunostained for the NMDA receptor subunit GluN2B and the postsynaptic scaffold PSD-95, together with the oligodendrocyte precursor markers PDGFRα. Confocal z-stacks were acquired and volumetrically reconstructed to quantify synaptic protein signal volume and puncta density within the PDGFRα-positive cellular volume. Contents raw_tiff/ — unmodified confocal z-stacks. imaris/ — processed Imaris (.ims) files containing surface and spot reconstructions used for volumetric quantification. quantification_source_data/ — per-cell signal volume and puncta density values exported from Imaris; these are the values plotted in the manuscript figures and tested in Supplementary Table S5.

The Darwin Tree of Life project has the goal to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. This is a collection of photographs of the samples included in the study, provided by the National History Museum (NHM).

Mosquito-Alert http://www.mosquitoalert.com/ is a cooperative citizen science observatory coordinated by different public research institutions. Its main objective is to monitor the spread of invasive species of mosquitoes, particularly the tiger mosquito and the yellow fever mosquito, vectors of global diseases like Zika, Dengue and Chikungunya. The Mosquito-Alert app allows citizens to report a possible finding of the targeted species or their breeding places on the public space by sending images. The app collects the GPS position and other related information along with the image. Afterwards, a team of entomology experts validates the images. The validation is sent back to the participant and published in a public map of observations.

The Darwin Tree of Life project has the goal to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. This is a collection of photographs of the samples included in the study, provided by the National History Museum (NHM).

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. This is a collection of the samples included in the study, provided by COPO at Earlham Institute.

Convergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and several 'core members' of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/Dishevelled (Dvl) and Van Gogh-like (Vangl)/Prickle (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane and keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz in Xenopus embryos. Pk inhibits the transition and functionally synergizes with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly but can be co-fractionated with Vangl. Collectively, we propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serve two functions: (1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and (2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt-induced dimerization of Fz and Ror.

Convergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and several ‘core members’ of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/Dishevelled (Dvl) and Van Gogh-like (Vangl)/Prickle (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane and keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz in Xenopus embryos. Pk inhibits the transition and functionally synergizes with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly but can be co-fractionated with Vangl. Collectively, we propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serve two functions: (1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and (2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt-induced dimerization of Fz and Ror.

Microscopy data for manuscript: "Palmitoylated Importin Alpha Regulates Mitotic Spindle Orientation Through Interaction NuMA". A study elucidating a novel role of the nuclear transport protein importin alpha in astral microtubule anchoring.

Cell state transitions underlie the emergence of diverse cell types and are traditionally defined by changes in gene expression. Yet these transitions also involve coordinated shifts in cell morphology and behaviour, which remain poorly characterized in densely packed epithelia. We developed a quantitative live-imaging and computational framework to track thousands of individual cells over time in the rapidly differentiating Xenopus mucociliary epithelium (MCE). From segmentations and trajectories, we extracted dynamic features—cell and nuclear shape, movement, and position—to create a time-resolved morphodynamic dataset spanning the full course of differentiation. While single features showed high noise and low separability of ground-truth cell types, supervised machine learning revealed that integrating time-resolved features robustly predicts final cell fate. Gradient-boosted trees and multinomial logistic regression achieved moderate but consistent accuracy, especially for abundant epithelial lineages. Key discriminants included normalized Z position, membrane–nucleus offset, and absolute experimental time, whereas movement contributed minimally to the results. Our data show that morphodynamic signatures encode predictive information about cell identity and provide a framework linking cellular dynamics with molecular state.