Intestinal organoids have emerged as the new paradigm for modelling the healthy and diseased intestine with patient-relevant properties. In this study, we show directed differentiation of induced pluripotent stem cells towards intestinal-like phenotype within a microfluidic device. iPSCs are cultured against a gel in microfluidic chips of the OrganoPlate, in which they undergo stepwise differentiation. Cells form a tubular structure, lose their stem cell markers and start expressing mature intestinal markers, including markers for Paneth cells, enterocytes and neuroendocrine cells. Tubes develop barrier properties as confirmed by transepithelial electrical resistance (TEER). Lastly, we show that tubules respond to pro-inflammatory cytokine triggers. The whole procedure for differentiation lasts 14 days, making it an efficient process to make patient-specific organoid tubules. We anticipate the usage of the platform for disease modelling and drug candidate screening.

Recent years have seen a dramatic increase in the application of organoids to developmental biology, biomedical and translational studies. Organoids are large structures with high phenotypic complexity and are imaged on a wide range of platforms, from simple benchtop stereoscopes to high-content confocal-based imaging systems. The large volumes of images, resulting from hundreds of organoids cultured at once, are becoming increasingly difficult to inspect and interpret. Hence, there is a pressing demand for a coding-free, intuitive and scalable solution that analyses such image data in an automated yet rapid manner. Here, we present MOrgAna, a Python-based software that implements machine learning to segment images, quantify and visualize morphological and fluorescence information of organoids across hundreds of images, each with one object, within minutes. Although the MOrgAna interface is developed for users with little to no programming experience, its modular structure makes it a customizable package for advanced users. We showcase the versatility of MOrgAna on several in vitro systems, each imaged with a different microscope, thus demonstrating the wide applicability of the software to diverse organoid types and biomedical studies.

Elastic effects can prevent the complete fusion of two drops, a phenomenon known as arrested coalescence. Here we provide a theoretical framework to understand this process in embryonic stem cell aggregates.

Introduction: Adequate signal to background ratios are critical for the implementation of fluorescence-guided surgery technologies. While local tracer administrations help to reduce the chance of systemic side effects, reduced spatial migration and non-specific tracer diffusion can impair the discrimination between the tissue of interest and the background. To combat background signals associated with local tracer administration, we explored a pretargeting concept aimed at quenching non-specific fluorescence signals. The efficacy of this concept was evaluated in an in vivo neuronal tracing set-up. Methods: Neuronal tracing was achieved using a wheat germ agglutinin (WGA) lectin . functionalized with an azide-containing Cy5 dye ( N 3 -Cy5-WGA ). A Cy7 quencher dye ( Cy7-DBCO ) was subsequently used to yield Cy7-Cy5-WGA , a compound wherein the Cy5 emission is quenched by Förster resonance energy transfer to Cy7. The photophysical properties of N 3 -Cy5-WGA and Cy7-Cy5-WGA were evaluated together with deactivation kinetics in situ, in vitro (Schwannoma cell culture) , ex vivo (muscle tissue from mice; used for dose optimization), and in vivo ( nervus ischiadicus in THY-1 YFP mice) . Results: In situ , conjugation of Cy7-DBCO to N 3 -Cy5-WGA resulted in >90% reduction of the Cy5 fluorescence signal intensity at 30 minutes after addition of the quencher. In cells, pretargeting with the N 3 -Cy5-WGA lectin yielded membranous staining, which could efficiently be deactivated by Cy7-DBCO over the course of 30 minutes (91% Cy5 signal decrease). In ex vivo muscle tissue, administration of Cy7-DBCO at the site where N 3 -Cy5-WGA was injected induced 80-90% quenching of the Cy5-related signal after 10-20 minutes, while the Cy7-related signal remained stable over time. In vivo, Cy7-DBCO effectively quenched the non-specific background signal up to 73% within 5 minutes, resulting in a 50% increase in the signal-to-background ratio between the nerve and injection site. Conclusion: The presented pretargeted fluorescence-quenching technology allowed fast and effective reduction of the background signal at the injection site, while preserving in vivo nerve visualization. While this proof-of-principle study was focused on imaging of nerves using a fluorescent WGA-lectin, the same concept could in the future also apply t...

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