Project description
3D sequencing-based microscopy for spatial molecular maps
Current molecular imaging and spatial transcriptomics techniques are expensive have limited throughput and are restricted by their inherent two-dimensional nature. The EU-funded VOLUMINEX project will develop a 3D sequencing-based microscopy method for creating spatial molecular maps using DNA barcode networks. This process begins with tissue samples and culminates in affordable molecular images, making advanced imaging more accessible to researchers and clinical diagnostics. The project will apply this technology to organoids with support from life scientists. Project partners will also develop algorithms to address the computational challenges. The goal is to make comprehensive spatial and transcriptomic imaging affordable and accessible.
Objective
Current molecular imaging and spatial transcriptomics methods are limited in throughput and affordability, and are constrained by inherent 2-dimensionality. We propose the Volumetric UMI Network Explorer (VOLUMINEX), a 3D implementation of sequencing-based microscopy. This radical alternative to optical imaging builds spatial molecular maps by sequencing DNA barcode networks where each node is a clonally amplified DNA patch, and each edge indicates inter-node proximity. The resulting network reveals gene identities along with their locations without a reference map. We propose an end-to-end pipeline starting with a tissue, followed by enzymatic processing steps, and ending with sequencing and a computational reconstruction to form a molecular image. We envision this procedure as an off-the-shelf commercial kit, offering an inexpensive alternative to advanced imaging instrumentation, expanding access to more researchers and potentially even clinical diagnostic settings. We are led by a Stockholm-based tech-dev team with seminal contributions to the field of sequencing-based microscopy, and a Stockholm-based company Single Technologies AB with a proprietary 3D sequencing device uniquely suited for validating our technology. We have partnered with an Utrecht-based team of life scientists to develop and deploy our technology on organoids, a rich controllable model tissue-like system perfect for exploring 3D biological imaging. Finally, at the heart of the project are undiscovered laws and physical principles which we aim to uncover and exploit with our Paris-based team of theoreticians, who will develop optimisation, graph theory, and machine learning algorithms to tackle the challenging computational problem of spatial reconstruction presented by sequencing-based microscopy. Through VOLUMINEX, we aim to kick off a new era of molecular imaging where comprehensive spatial and transcriptomic data is accessible, affordable, and 3-dimensional.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: https://op.europa.eu/en/web/eu-vocabularies/euroscivoc.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: https://op.europa.eu/en/web/eu-vocabularies/euroscivoc.
- natural sciencesbiological sciencesgeneticsDNA
- natural sciencesphysical sciencesopticsmicroscopy
- social scienceslaw
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Keywords
Programme(s)
- HORIZON.3.1 - The European Innovation Council (EIC) Main Programme
Call for proposal
(opens in new window) HORIZON-EIC-2024-PATHFINDEROPEN-01
See other projects for this callFunding Scheme
HORIZON-EIC - HORIZON EIC GrantsCoordinator
100 44 Stockholm
Sweden