WP4
Modelling mechanical properties and open software for data processing
Duration: months 4-44
Lead beneficiary: INSERM
Objectives: the main goals of this WP are to provide a generalised mechanical model to describe cell and tissue mechanics and to develop multi-platform, open source software for the automatic analysis and visualisation of AFM mechanical data.
To define essential parameters to model cell and tissue mechanics. These include structural components, pre-stress, extra- and intercellular adhesion among others.
Task 4.1. Development of a mechanical model to describe the viscoelastic response of cells and tissues.
Task leader: INSERM
The model will also include their mechanical heterogeneity, dependence of cellular physiological state (cell cycle, cytoskeletal interventions...) and disease.
Task 4.2. Open source, data processing software through network-wide determination of the required features.
Task leader: UB
The data processing software will feature selection of approach and retract curves, various contact models (pyramidal, spherical, bottom correction...), spring constant and deflection sensitivity correction factors, virtual deflection correction... It will be automatised, robust, multi-platform and open source. (Lead UB, CNRS, UMIL, INSERM)
Task 4.3. Definition of a universal file format for exporting of raw data from mechanical AFM measurements.
Task leader: CEA
The universal format will provide the basic means for data sharing across laboratories and will include measurement parameters such as the date and time of acquisition, cantilever properties, system sensitivities, tip geometry, used instruments, calibration method, description of the sample, temperature, etc. (Lead CEA-IBS, CNRS,UB, INSERM)
Task 4.4. Definition of methods to visualise raw and processed data.
Task leader: CNRS
Mechanical data are highly multidimensional (position on the sample, time, cell type) and ask for smart algorithms to reduce dimensionality for display and analysis. This may involve 3d graphing techniques, but also multi-dimensional fitting, modelling, and statistical tests.
Task 4.5. Creation of a database with raw data from mechanical tests (force curves) for cross-laboratory analysis.
Task leader: UMIL
This will follow the guidelines of the Open Research Data Pilot to share, deposit and maximise the access to all data acquired during the project. A data management plan (DMP) will be defined at month 6 and updated during the project. It may include external advice from experts in related fields.
(Lead INSERM, CEA-IBS, UB,UMIL)