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Data Science Centre

Managing, analysing and sharing data at scale

Bioimage analysis services

Service mission

The Bioimage Analysis Service Team supports EMBL scientists, visitors, and service users in extracting biophysically meaningful information from microscopy data in a reproducible manner. To achieve this, the team develops and deploys analysis workflows on appropriate computational infrastructure. Additionally, regular training workshops empower scientists to perform image data analysis independently. This service is built on strong collaborations with EMBL’s microscopy facilities and IT services.

How we work

Our main focus is the development of reproducible bioimage analysis workflows. To this end, we rely on GitLab for project management, the DMA for data management, and Nextflow for deploying workflows on high performance compute infrastructure.

We develop and deliver training courses aiming at empowering life scientist to perform image analysis on their own. Here, our current focus is on teaching python scripting based bioimage analysis, using publicly accessible training material that we develop in collaboration with a growing international community of bioimage analysts.

We are committed towards strengthening professional bioimage analysis. To do so, we actively participate in the GloBIAS initiative and we regularly run EMBO workshops for bioimage analysts. Realising that a common, powerful and well supported image data format would be a game changer for conducting professional bioimage analysis we are actively supporting the development and use of OME-Zarr. Moreover, together with NFDI4BIOIMAGE we are working on leveraging cloud computing resources such as abcDesktop and Galaxy for providing open and unified access to bioimage analysis tools.