Cellular & Molecular Imaging

This repository contains high-resolution confocal microscopy datasets of mosquito larval midgut tissues exposed to Bacillus thuringiensis Cry toxins and fluorescent markers for cellular organelles. The data were collected using an Olympus FV1000 confocal laser scanning microscope with a 60X oil immersion objective and a pixel size of 59 nm. The datasets include images of Cry toxins labeled with Alexa Fluor dyes and markers such as SiR-Actin, SiR-Lysosomes, MitoTracker, FM4-64, ER-Tracker, and DAPI. Each dataset represents independent replicates from midgut tissue dissections of at least five larvae per experimental condition.

imaging method

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).

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.

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).

Advances in biological imaging have transformed our understanding of living systems, yet access to state-of-the-art microscopy remains out of reach for many researchers. This is specially true for those without direct access to specialized optics laboratories or those working with non-model organisms. To overcome these barriers, we developed Flamingo: an adaptable, modular, and portable light sheet microscope designed for diverse research environments. Flamingo enables dynamic reconfiguration to suit a wide range of imaging needs and facilitates high-quality data acquisition directly in biological labs or field stations. We utilized Flamingo to image a range of intact, living, and cleared samples, demonstrating its versatility across various sample types and experimental conditions. Our fully assembled, ready-to-use Flamingo empowers biologists to pursue novel research questions and democratizes access to advanced microscopy.

Microscopy images and movies used for our publication "The increase of Cyclin A/cdk activity and of FAM122A-dependent inhibition of PP2A-B55 are key events to trigger mitosis"

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).

In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 µm laterally, 3.3 µm axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.

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).