Biology subjects

de Medeiros, G.

Publications and source records attributed to de Medeiros, G..

4 recordsLinked to original sources

bioRxiv2023

Open top multi sample dual view light sheet microscope for live imaging of large multicellular systems

Multicellular systems grow over the course of weeks from single cells to tissues or even full organisms composed of several thousands of cells, making live imaging of such samples challenging. To bridge these wide spatiotemporal scales, we present an open top dual view and dual illumination light sheet microscope dedicated for live imaging of large specimens at single cell resolution. The novel configuration of objectives together with a flexible and customizable multi-well mounting system combines dual view with high throughput multi-position imaging. We use the newly developed microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.

developmental biology↗

bioRxiv2023

OME-Zarr: a cloud-optimized bioimaging file format with international community support

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself - OME-Zarr - along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

bioinformatics↗

bioRxiv2021

Multiscale light-sheet organoid imaging framework

Organoids provide an accessible in-vitro system to mimic the dynamics of tissue regeneration and development. However, long-term live-imaging of organoids remains challenging. Here we present an experimental and image-processing framework capable of turning long-term light-sheet imaging of intestinal organoids into digital organoids. The framework combines specific imaging optimization combined with data processing via deep learning techniques to segment single organoids, their lumen, cells and nuclei in 3D over long periods of time. By linking lineage trees with corresponding 3D segmentation meshes for each organoid, the extracted information is visualized using a web-based "Digital Organoid Viewer" tool allowing unique understanding of the multivariate and multiscale data. We also show backtracking of cells of interest, providing detailed information about their history within entire organoid contexts. Furthermore, we show cytokinesis failure of regenerative cells and that these cells never reside in the intestinal crypt, hinting at a tissue scale control on cellular fidelity.

cell biology↗

bioRxiv2018

Instantaneous isotropic volumetric imaging of fast biological processes

Capturing highly dynamic biological processes at sub-cellular resolution is a recurring challenge in biology. Here we show that combining selective volume illumination with simultaneous acquisition of orthogonal light-fields yields 3D images with high, isotropic spatial resolution and free of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate Medaka heart and blood flow imaging with single-cell resolution and free of motion artefacts at volume rates up to 200Hz.

bioengineering↗