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RE2Vital - REuse and REproducibility of intraVITAL microscopy via open data practices in image-driven immunological research



González F. S.


Krause R.


Pizzagalli D. U.



The immune system involves complex biological processes with a strong dynamic component, such as cell migration and cell-to-cell interaction. Imaging technologies are becoming pivotal to study these processes. Of note, in the last two decades, intravital microscopy (IVM) allowed to unravel unprecedented details on the cellular dynamics of the immune system. IVM generates multidimensional data (3d videos with multiple acquisition channels), which are analyzed by performing cell tracking and by computing measures of cell motility/interaction.
Unfortunately, IVM data, metadata, and tracks typically remain stored in private servers with restricted access; only part of it being published as supplementary materials along with manuscripts, mainly for visualization purposes. This hampers data reusability, reproducibility, and further analyses to answer additional questions outside the original goal. Moreover, the application of data mining methods is particularly affected, as large datasets are typically required.
To overcome these limitations, thanks to a SNSF funding and an international network of 15 world-class laboratories, we created IMMUNEMAP, an Open Data platform for IVM data dedicated to immunological processes. Currently, IMMUNEMAP counts more than 350 IVM videos and 24’000 single-cell trajectories.
Here, we aim at advancing and fully anchoring Open Data practices with IMMUNEMAP by:
a) Consolidating the functionalities of IMMUNEMAP including findability and interoperability;
b) Promoting data exchange between immunology and computer vision communities, thus expanding the network of partners;
c) Educating researchers to adopt open protocols that safeguard reproducibility.
These advancements will foster the availability of IVM data under the FAIR principles and allow data-driven immunological studies.

Additional information

Start date
End date
24 Months
Funding sources
Swissuniversities Swiss Confederation
swissuniversities / Open Research Data calls / Measure A1, Track B: Establish projects