Bioimaging Research Fellow: Open-Source 3D Imaging

EURAXESS Ireland; Faro; Hybrid; EUR 12,000 - 18,000; Full time

Job summary

CCMAR – Centro de Ciências do Mar do Algarve invites applications for a Research Fellowship in Bioimaging under the IMAGINE project. A Master’s degree holder is eligible for a non-conductive fellowship supporting advanced imaging tool development and open-source software integration.

The position focuses on building low-cost optical imaging systems, 3D whole-body imaging, and collaboration across CCMAR, UAlg, and international partners, including open-source plugin development for Napari/ImageJ

Qualifications

• Bachelor’s degree in Physics, Engineering, Biomedical Engineering, or a related discipline.
• Master’s degree in Physics, Engineering, Biomedical Engineering, or a related discipline.
• Non-compliance justifies exclusion from the procedure.

Responsibilities

• Design and build an improved version of QBI’s open-source, low-cost 3D optical imaging system, including optical projection tomography and lightsheet microscopy modules.
• Prototype components using 3D printing.
• Develop advanced illumination and detection strategies to reduce scattering effects.
• Accelerate scans and automate image analysis by integrating AI methods in collaboration with QBI team members.
• Integrate the developed methods into user-friendly plugins for Napari and/or ImageJ, ensuring open-source availability and community adoption.
• Test the system using phantom, live developing/adult zebrafish, and marine organisms.
• Disseminate results via high-impact publications, open-source code releases and presentations at international conferences.
• Develop outreach activities and participate in science-communication activities, helping to promote open science and public education in microscopy and marine biology.
• Collaborate with other groups at CCMAR, UAlg and beyond (e.g. EMBL).

Skills

Hands-on optical imaging

Python/C++ programming

Education

Bachelor’s degree in Physics/Engineering/Biomedical Engineering

Master’s degree in Physics/Engineering/Biomedical Engineering

Job description

CCMAR – Centro de Ciências do Mar do Algarve invites applications for a Research Fellowship in Bioimaging under the IMAGINE project. A Master’s degree holder is eligible for a non-conductive fellowship supporting advanced imaging tool development and open-source software integration.

The position focuses on building low-cost optical imaging systems, 3D whole-body imaging, and collaboration across CCMAR, UAlg, and international partners, including open-source plugin development for Napari/ImageJ