Work Packages

WP1: Gel Polony Chemistry

Led by KI, this work package aims to optimize the conditions for gel formation and bridge amplification, resulting in the growth of polonies within a 3D hydrogel structure. ST provides assistance with their expertise in gel formulation and imaging, while SU are tasked with creating a simulation model of the polony growth from the bridge amplification data provided by KI.

WP2: In Situ 3D Networks

Led by KTH, this work package aims to build upon the work in WP1 to create a robust prototype which is easily verified without tissue. The KTH team will lead experimental and computational development, supported by KI who will grow polonies in the hydrogels. ST will also assist with confocal imaging, while SU will provide simulation modelling and reconstruction.

WP3: In Situ Validation

Led by ST, this work package aims to perform in situ validation of the networks formation and molecular capture processes. State-of-the-art imaging and sequencing will be used to evaluate the uniformity and efficiency of primer incorporation, polony formation and network growth within the hydrogel matrix.

WP4: Organoid Adaptation

Led by PMC, this work package aims to apply the polony growth and network formation methods to organoid models and to conduct detailed spatial transcriptomic analysis in complex 3D tissue models. ST will provide in situ validation while KTH will assist with network formation methods.

WP5: Algorithms for Spatial Reconstruction

Led by SU, this work package aims to develop and test scalable and robust algorithms for reconstructing 3D spatial configurations of polony locations from proximity networks, and accurately mapping the spatial transcriptome.

WP6: Communication and Dissemination

Led by KTH, this work package aims to strategically promote and share the VOLUMINEX results by ensuring the findings reach their appropriate target audiences and by engaging with stakeholders. Communication channels, such as this website and LinkedIn, will be used to create a sustainable flow of project information to the public.

WP7: Coordination and Project Management

Led by KTH, this work package aims to ensure timely execution of project tasks within the project timeframe. In addition to project management, tasks include IP management, the establishment of a data management plan, risk and ethics management, and project reporting to the European Innovation Council. A project coordination board (PCB) meets monthly, with representatives from each VOLUMINEX partner, to monitor project progress, discuss the latest results from the work packages and to make strategic decisions for the future of VOLUMINEX.