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Data science and electron nanoscopy come together at 18th LCDS meeting

Electron nanoscopy produces vast amounts of data. How can methods from the field of data science help in processing and analysing it? Researchers from LCDS, LIACS and NeCEN came together at the 18th LCDS meeting to explore this question.

New techniques in the field of electron nanoscopy offer unique possibilities to study biological structures. By flash freezing biological samples and making images from different angles, very detailed 3D-models can be made. To perform this kind of experiments, researchers can turn to open access facility NeCEN, which houses two state-of-the-art microscopes.

Computational needs

Ariane Briegel

Obviously, this type of research, which involves high resolution imaging, produces large amounts of data. The challenges in terms of data management and analysis were addressed at the 18th LCDS meeting, which took place on 18 April 2017.

The research field of electron nanoscopy, as well as its computational aspects and needs, were introduced by Roman Koning (LUMC). Then Ludo Renault (NeCEN) spoke about the way in which ever growing amounts of data are handled and managed at NeCEN, and Ariane Briegel (IBL) discussed the challenges of data processing in her research on the sensory systems of bacteria.  

Bio-science software

In the second part of the meeting, computer scientists from LIACS discussed computational methods and hardware which are relevant to electron nanoscopy. Fons Verbeek presented the work of Enrique Larios, his former PhD student: CytomicsDB. This database comprises a metadata validation system which can be used to ensure the consistency, integrity and reliability of the data managed in experiments.

Kristian Rietveld discussed Leiden Life Sciences Cluster (LLSC), a cluster computer that is used for the development and deployment of bio-science software. This can significantly reduce computation time, said Rietveld: in the future, the whole process from data acquisition to making a high resolution 3D model could be a matter of minutes instead of days.


The talks made clear that there are many areas in which NeCEN, LIACS and LCDS may be able to join efforts. With new equipment and imaging in ever higher resolutions, the need for computational solutions in the field of electron nanoscopy is increasing. During this meeting, the foundations for future contacts and collaborations were laid. 


During its monthly meetings, the Leiden Centre of Data Science brings together data scientists and researchers/professionals from other disciplines. Each of the events is centered around a specific topic or field of study. If you would like to stay updated on the events LCDS organizes, please subscribe to our mailing list.