The Journal of Open Source Software, Journal Year: 2025, Volume and Issue: 10(109), P. 7882 - 7882
Published: May 17, 2025
Language: Английский
Histochemistry and Cell Biology, Journal Year: 2023, Volume and Issue: 160(3), P. 223 - 251
Published: July 10, 2023
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 institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself-OME-Zarr-along with tools data resources available today increase FAIR access remove barriers in scientific process. The current momentum offers an opportunity unify key component domain-the that underlies so many personal, institutional, global management analysis tasks.
Language: Английский
Citations
63
Cell, Journal Year: 2024, Volume and Issue: 187(25), P. 7045 - 7063
Published: Dec. 1, 2024
Cells are essential to understanding health and disease, yet traditional models fall short of modeling simulating their function behavior. Advances in AI omics offer groundbreaking opportunities create an virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent simulate the behavior molecules, cells, tissues across diverse states. This Perspective provides vision on design how collaborative efforts build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, guiding experimental studies, offering new for cellular functions fostering interdisciplinary collaborations open science.
Language: Английский
Citations
21
Nature Reviews Clinical Oncology, Journal Year: 2024, Volume and Issue: 21(9), P. 660 - 674
Published: July 23, 2024
Language: Английский
Citations
20
Nature Methods, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 27, 2024
Language: Английский
Citations
16
Nature Methods, Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 19, 2024
Language: Английский
Citations
12
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: June 11, 2024
Abstract Spatial omics data allow in-depth analysis of tissue architectures, opening new opportunities for biological discovery. In particular, imaging techniques offer single-cell resolutions, providing essential insights into cellular organizations and dynamics. Yet, the complexity such presents analytical challenges demands substantial computing resources. Moreover, proliferation diverse spatial technologies, as Xenium, MERSCOPE, CosMX in spatial-transcriptomics, MACSima PhenoCycler multiplex imaging, hinders generality existing tools. We introduce Sopa ( https://github.com/gustaveroussy/sopa ), a technology-invariant, memory-efficient pipeline with unified visualizer all image-based omics. Built upon universal SpatialData framework, optimizes tasks like segmentation, transcript/channel aggregation, annotation, geometric/spatial analysis. Its output includes user-friendly web reports files, well comprehensive files Overall, represents significant step toward unifying analysis, enabling more understanding interactions organization systems.
Language: Английский
Citations
9
Cell, Journal Year: 2025, Volume and Issue: unknown
Published: March 1, 2025
The organs of many female animals are remodeled by reproduction. Using the mouse intestine, a striking and tractable model organ resizing, we find that reproductive remodeling is anticipatory distinct from diet- or microbiota-induced resizing. Reproductive involves partially irreversible elongation small intestine fully reversible growth its epithelial villi, associated with an expansion isthmus progenitors accelerated enterocyte migration. We identify induction SGLT3a transporter in subset enterocytes as early hallmark. Electrophysiological genetic interrogations indicate does not sustain digestive functions health; rather, it detects protons sodium to extrinsically support adjacent Fgfbp1-positive progenitors, promoting villus growth. Our findings reveal unanticipated specificity physiological remodeling. suggest organ- state-specific programs could be leveraged improve pregnancy outcomes prevent maladaptive consequences such
Language: Английский
Citations
1
Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(11)
Published: Oct. 16, 2023
Abstract Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information any data type on spatial scales ranging from subcellular to organismal. From technology development perspective, is highly interdisciplinary that integrates imaging omics, molecular analyses, sequencing mass spectrometry, image analysis bioinformatics. The emergence this not only opened window into biology, but also created multiple opportunities, questions, challenges method developers. Here, we provide the perspective developers what makes unique. After providing brief overview state art, discuss technological enablers present our vision about future applications impact melting pot.
Language: Английский
Citations
18
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Nov. 27, 2023
Emerging spatial omics technologies continue to advance the molecular mapping of tissue architecture and investigation gene regulation cellular crosstalk, which in turn provide new mechanistic insights into a wide range biological processes diseases. Such an increasingly large amount information content at multiple scales. However, representing harmonizing diverse datasets efficiently, including combining modalities or scales scalable flexible manner, remains substantial challenge. Here, we present Giotto Suite, suite open-source software packages that underlies fully modular integrated data analysis toolbox. At its core, Suite is centered around innovative technology-agnostic framework embedded R environment, allows representation integration virtually any type resolution. In addition, provides both extensible end-to-end solutions for analysis, integration, visualization. integrates molecular, morphology, spatial, annotated feature create responsive workflow multi-scale, multi-omic analyses, as demonstrated here by applications several state-of-the-art technologies. Furthermore, builds upon interoperable interfaces structures bridge established fields genomics science, thereby enabling independent developers custom-engineered pipelines. As such, creates immersive ecosystem analysis.
Language: Английский
Citations
14
Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)
Published: June 11, 2024
Abstract The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification encompass more detailed view cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements multiple components—transcriptome, proteome, chromatin, epigenetic modifications metabolites—within single including spatial contexts within tissues. This led generation complex multiscale datasets that can include multimodal from same cells or mix paired unpaired modalities. Modern machine learning (ML) techniques for integration “omics” data without need extensive independent modelling each modality. review focuses recent ML integrative approaches applied immunological studies. We highlight importance methods creating unified representation collections, particularly profiling technologies. Finally, we discuss challenges holistic how they will be instrumental development common coordinate framework studies, thereby accelerating research enabling discoveries computational immunology field.
Language: Английский
Citations
5