Microscopy Imaging Specialist

at  Amsterdam UMC

ABOUT THE PROJECT

Join our innovative team at the Microscopy Core Facility Cellular Imaging, where we support a wide range of research projects of 500+ users through advanced microscopy and cutting-edge imaging techniques. We handle diverse imaging challenges, from processing large image datasets to managing high-throughput screens with thousands of images. Our integrated framework, powered by OMERO and our recently published BIOMERO, leverages high-performance computing (HPC) environments for efficient, automated image analysis.
We aim to expand our capabilities and enhance our framework by developing workflows that are Findable, Accessible, Interoperable, and Reusable (FAIR). These workflows will support various imaging analysis tasks and incorporate external tools, including large language models, to meet the evolving needs of our research community NL-BioImaging.

PROFILE

We are seeking a microscopy imaging specialist who possesses:

• A Master’s degree in a relevant field such as Computer Science, Bioinformatics, Biomedical Engineering, or similar;
• (Preferably) documented background in image analysis, with experience in handling large datasets or high-throughput imaging projects;
• Proficiency in Python and experience with GitHub and Docker;
• Familiarity with HPC environments and job management tools like SLURM;
• Ability to develop and extend applications, particularly within existing open-source frameworks;
• (Preferably) knowledge of image analysis software such as ImageJ, QuPath, CellProfiler, and MATLAB;
• Good communication skills, with the ability to engage with both technical and non-technical stakeholders (users of the microscopy core facility).

As an Imaging Specialist, you will:

• Work with diverse imaging types, with a focus on fluorescence imaging, handling both large-scale and high-throughput image sets;
• Design and refine diverse advanced image analysis workflows, deploying them in HPC environments;
• Collaborate with national (Nl-BioImaging) and international (Euro-BioImaging) partners to understand user needs and integrate existing external workflows into our system;
• Contribute to open and transparent science by making the image analysis workflows FAIR-compliant;
• Enhance and optimize our imaging framework to support new research applications and improve performance;
• Document, communicate and disseminate your work effectively, contributing to the general advancement of imaging technologies in research and clinical settings.