Luca Marconato
A5025605769- Biomedical and Engineering Education
- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Reproductive System and Pregnancy
- Birth, Development, and Health
- Pregnancy and preeclampsia studies
- Geographic Information Systems Studies
- Vehicle emissions and performance
- Image Processing Techniques and Applications
- 3D Modeling in Geospatial Applications
- Air Quality Monitoring and Forecasting
- Health, Environment, Cognitive Aging
European Molecular Biology Laboratory
2023-2024
German Cancer Research Center
2022-2023
Heidelberg University
2022-2023
University of Cambridge
2022
Abstract The relationship between the human placenta—the extraembryonic organ made by fetus, and decidua—the mucosal layer of uterus, is essential to nurture protect fetus during pregnancy. Extravillous trophoblast cells (EVTs) derived from placental villi infiltrate decidua, transforming maternal arteries into high-conductance vessels 1 . Defects in invasion arterial transformation established early pregnancy underlie common disorders such as pre-eclampsia 2 Here we have generated a...
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...
Abstract Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling uni- and multimodal spatial datasets remains a challenge owing to large data volumes, heterogeneity types lack flexible, spatially aware structures. Here we introduce SpatialData, framework that establishes unified extensible multiplatform file-format, lazy representation larger-than-memory data, transformations alignment common coordinate systems. SpatialData...
Abstract Spatially resolved omics technologies are transforming our understanding of biological tissues. However, handling uni- and multi-modal spatial datasets remains a challenge owing to large volumes data, heterogeneous data types the lack unified spatially-aware structures. Here, we introduce SpatialData, framework that establishes extensible multi-platform file-format, lazy representation larger-than-memory transformations, alignment common coordinate systems. SpatialData facilitates...
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...
The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter University of Zurich, brought together an international group researchers and developers to develop ecosystem around open, scalable, FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing OME-Zarr specification, (2) enabling workflow interoperability by integrating image processing tasks across multiple open-source frameworks, (3) expanding Java support for...
The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter University of Zurich, brought together an international group researchers and developers to develop ecosystem around open, scalable, FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing OME-Zarr specification, (2) enabling workflow interoperability by integrating image processing tasks across multiple open-source frameworks, (3) expanding Java support for...
Abstract The relationship between the human placenta, extraembryonic organ built by fetus, and decidua, mucosal layer of uterus, is essential to nurture protect fetus during pregnancy. Extravillous trophoblast cells (EVTs) anchor placenta infiltrate transforming maternal arteries into high conductance vessels. Defects in invasion arterial transformation established early pregnancy underlie common disorders such as pre-eclampsia. Despite its importance, how EVT regulated humans still unclear...
Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images key to training developing new methods, but access such data is often hindered by the lack of standards sharing datasets. We brought together community experts in a workshop develop guidelines improve reuse bioimages annotations AI applications. These include on formats, metadata, presentation sharing, incentives generate positive that MIFA (Metadata, Incentives,...
During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The were organized in five workgroups and included benchmarking, pipelines, transcriptomics, proteomics, multi-omics cell-cell communication. Most tools methods considered context Python ecosystem for (SpatialData) single-cell (scverse)
This pre-print is aimed at sharing the results of "1st SpatialData workshop," an in-person event organized by team and funded Chan Zuckerberg Initiative (CZI) that brought together expertise from different fields, including methods developers a variety tools for single-cell spatial omics. The purpose to explore new directions advance field By leveraging multiple programming languages, Python, R, JavaScript, focuses on four central hackathon tracks: R interoperability: track aims enhance...