Cellular & Molecular Imaging

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).

Raw image filed for figure 3, 4, and 5 of the manuscript.

Upon activation of ASC-containing inflammasomes, intracellular molecular aggregates (ASC specks) are assembled and released from myeloid cells into the extracellular space where they enhance the aggregation of Aβ amyloid in Alzheimer’s disease. This raises the question whether ASC is involved in additional aggregation proteinopathies. In this study we report that ASC governs the extent of inflammation-induced amyloid A (AA) amyloidosis, a systemic disease caused by the aggregation and peripheral deposition of the acute-phase reactant serum amyloid A (SAA).

DNA double-strand breaks are dangerous lesions in mitosis as they can lead to mis-segregation of acentric chromosome fragments. We previously showed that MDC1 and TOPBP1 are critically implicated in the maintenance of chromosomal stability during mitosis. In this study we reveal that the CIP2A protein is mediating TOPBP1 accumulation at sites of DNA breaks in mitosis. Furthermore, we show that CIP2A deficient cells are sensitive to DNA breaks and chromosmally unstable.

Drosophila notum containing SOP cells (labelled with RFP-Pon). Stained for total tubulin and poly-glutamylated tubulin.

Large-area scanning electron microscopy (SEM) of mouse liver and pancreatic islet from a two-phase weight-cycling and caloric-restriction dietary study, acquired at 5 nm pixel size. Twenty-eight large-area mosaics are included. Files are organised into one folder per diet regimen, and each file name also carries that regimen as phase1-phase2, where AL = ad libitum control diet, CR = calorie restriction and HF = high-fat diet. The full experimental design and the results derived from these images are described in the associated publication.

This dataset shows calcium signalling waves in a MDCK epithelium. The cells stably express GCaMP6S, a GFP-based intracellular calcium sensor. Imaging data courtesy of Yasuyuki Fujita (Y. Takeuchi et al., “Calcium Wave Promotes Cell Extrusion,” Current Biology, vol. 30, no. 4. Elsevier BV, pp. 670-681.e6, Feb. 2020. doi: 10.1016/j.cub.2019.11.089). Collective event analysis has been performed using ARCOS (P. A. Gagliardi et al., “Automatic detection of spatio-temporal signaling patterns in cell collectives,” Journal of Cell Biology, vol. 222, no. 10. Rockefeller University Press, Jul. 27, 2023. doi: 10.1083/jcb.202207048). The analysis scripts and results corresponding to the raw data published here are accessible online (Maciej Dobrzynski, “ARCOS, a computational approach for automatic recognition of collective signalling.” Mendeley, Apr. 26, 2023. doi: 10.17632/8GCNCG6ZKT.3). Additionally, the dataset has been used to showcase the capabilities of conv-paint, an interactive pixel classification tool for napari. Data dimensions: [t,y,x] -> [300,1024,1024] Pixel resolution: 0.86µm/px (880.64μm total) Time resolution: 5sec/frame (25min total) Filetype: TIFF

machine learning

3D cell cultures are indispensable in recapitulating in vivo environments. Among the many 3D culture methods, culturing adherent cells on hydrogel beads to form spheroid-like structures is a powerful strategy for maintaining high cell viability and functions in the adherent states. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high throughput, scalable 3D imaging flow cytometry platform for analyzing spheroid models. This platform is realized by integrating a single objective fluorescence light-sheet microscopy with a microfluidic device that combines hydrodynamic and acoustofluidic focusing techniques. This integration enabled unprecedentedly high-throughput and scalable optofluidic 3D imaging, processing 1310 spheroids consisting of 28 117 cells per minute. The large dataset obtained enables precise quantification and comparison of the nuclear morphology of adhering and suspended cells, revealing that the adhering cells have smaller nuclei with less rounded surfaces. This platform's high throughput, robustness, and precision for analyzing the morphology of subcellular structures in 3D culture models hold promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.

Image-data, ilastik pixel classification project, CellProfiler pipeline and MATLAB code enabling the local correlation quotient analysis described in the paper entitled: In the murine and bovine maternal mammary gland signal transducer and activator of transcription 3 is activated in clusters of epithelial cells around the day of birth.