Job Information
Organisation/Company: Champalimaud Foundation
Research Field: Technology
Researcher Profile: Recognised Researcher (R2)
Positions: PhD Positions
Application Deadline: 30 Sep 2026 - 17:00 (Europe/Lisbon)
Country: Portugal
Type of Contract: Other
Type of Contract Extra Information: Fellowship
Job Status: Full-time
Hours Per Week: 40
Is the job funded through the EU Research Framework Programme? Not funded by a EU programme
Is the Job related to staff position within a Research Infrastructure? No
Offer Description
The Champalimaud Foundation (Fundacao D. Anna de Sommer Champalimaud e Dr. Carlos Montez Champalimaud), a private, non-profit biomedical research and clinical institution in Lisbon, Portugal, is seeking a Light Microscopy Imaging Specialist to join the Advanced BioImaging and BioOptics Experimental (ABBE) Platform within Champalimaud Research.
The ABBE Platform is a highly active scientific imaging platform supporting fundamental, translational and technology-development projects across neuroscience, cancer research and other areas of life science. The facility currently provides access to 10 advanced imaging systems, supports approximately 170 users per year and records more than 20,000 booked instrument hours annually. ABBE is actively engaged with the Portuguese Platform of BioImaging (PPBI), Euro-BioImaging and Global BioImaging.
The platform combines open-access infrastructure with expert scientific consultation, hands-on training, quality-controlled instrumentation, image analysis support and technology development.
We are looking for a highly motivated, collaborative and service-oriented PhD-level specialist who will work as part of the ABBE team. The successful candidate will support users from initial experimental planning through image acquisition and first-line analysis, with particular emphasis on confocal and super-resolution microscopy, deep-tissue imaging, light-sheet microscopy and quantitative image analysis. The role is designed for a scientist who enjoys enabling the work of others while remaining scientifically engaged with challenging imaging questions and new technology
Main Responsibilities
- Provide scientific consultation for a broad range of imaging projects, helping users translate biological questions into robust microscopy strategies, including appropriate controls, acquisition parameters and sample-preparation requirements.
- Train users in basic and advanced light microscopy, with the objective of developing independent, critical and responsible microscope users. Training will include one-to-one sessions as well as structured courses and workshops.
- Provide expert support in confocal microscopy, super-resolution imaging, deep-tissue microscopy, light-sheet microscopy, widefield imaging and automated slide scanning, depending on experience and project needs.
- Support imaging of both living and fixed samples, including small model organisms and large cleared specimens, and advise on experimental constraints such as phototoxicity, sampling, optical aberrations and refractive-index mismatching.
- Provide first-line support for image visualization, 3D reconstruction, quantification and analysis using open-source and commercial software. ABBE currently offers IMARIS CF, Arivis and Aivia, in addition to community tools such as Fiji/ImageJ and related open-source solutions.
- Perform routine system performance checks, quality control, preventive maintenance and troubleshooting; document instrument performance and coordinate with manufacturers/service engineers when intervention is required.
- Contribute to the implementation, validation and optimization of new imaging technologies, workflows and applications, including integration of new hardware and software into the platform.
- Contribute to ABBE microscopy and image-analysis courses, workshops, user documentation, standard operating procedures and internal knowledge sharing.
- Coordinate with other institutional platforms when projects require integrated workflows, for example pathology/histology, model-organism facilities, scientific software, hardware development, IT or sample-preparation services.
- Support external-access and collaborative projects associated with national and European research-infrastructure activities, as appropriate to the role and platform priorities.
Scientific contribution beyond the core service mission is encouraged. When compatible with service priorities, the specialist may contribute to technology-development projects, collaborative research with internal or external groups, and academia-industry activities. Contributions that meet standard scientific authorship criteria will be recognized accordingly.
Platform Environment
The ABBE instrumentation portfolio is designed to support multiscale imaging, from subcellular and super-resolution applications to whole-organ and small-organism imaging. Current capabilities include high-end widefield microscopy and automated slide scanning, multiple laser-scanning confocal systems with advanced detectors and extended-resolution capabilities, and complementary light-sheet systems for long-term imaging of small living specimens and large optically cleared samples. The platform is expanding further to address high-speed live-cell, super-resolution and advanced quantitative imaging needs.
For image analysis, ABBE provides access to three complementary commercial platforms - IMARIS CF, Arivis and Aivia - alongside open-source analysis environments. This combination enables flexible support for segmentation, tracking, 3D/4D visualization, quantitative analysis and increasingly AI-assisted workflows.
Employer: Champalimaud Foundation
Department: Advanced BioImaging and BioOptics Experimental Platform (ABBE Platform)
Number and type of fellowships or contracts to be awarded: 1 full-time position - fellowship
Application start date: September 1st, 2026
Application closing date: September 30th, 2026
Expected position starting date: January 1st, 2027
Where to apply
Requirements
Research Field: Technology
Education Level: PhD or equivalent
Skills/Qualifications
Required Education Level
PhD degree in Biology, Physics, Engineering, Biophysics, or a related field. Applications will also be considered from candidates who are in the final stage of their PhD and have a confirmed thesis submission date no later than 31 December 2026.
Minimum Qualifications
- Candidates must hold a PhD in Biology, Physics, Engineering, Biophysics, or a related discipline. Candidates who have not yet formally completed their PhD may also apply, provided that they are in the final stage of their doctoral studies and can demonstrate that thesis submission is scheduled for no later than 31 December 2026.
- Solid hands-on experience in advanced light microscopy and a clear understanding of the principles that govern image formation, resolution, sampling, signal-to-noise ratio and phototoxicity.
- Experience supporting or independently conducting microscopy experiments in a research environment.
- Fluency in English, the working language of Champalimaud Research.
Specific Requirements
Essential Skills and Competencies
- Practical experience with confocal microscopy and at least one additional advanced modality relevant to the ABBE portfolio (for example light-sheet, multiphoton/deep-tissue, super-resolution, high-content or advanced widefield imaging).
- Ability to optimize acquisition conditions and troubleshoot common imaging problems involving sample preparation, optics, detectors, illumination, alignment, environmental control or acquisition software.
- Experience with quantitative image analysis, including 3D/4D visualization, segmentation, measurement and data interpretation using open-source and/or commercial software.
- Programming or scripting skills in Python, Java, C/C++ or similar languages, particularly for image analysis, workflow automation, microscope control or hardware integration.
- Ability to explain complex technical concepts clearly to researchers with different levels of microscopy experience and from different scientific backgrounds.
- Strong service orientation: willingness to understand the scientific question behind each request and to help users choose the most appropriate and reproducible approach rather than simply execute an acquisition request.
- Ability to work independently while contributing reliably to a small expert team, prioritize multiple user projects, document work and communicate limitations or risks early.
- Proactive attitude toward learning new technologies, improving workflows and sharing knowledge with colleagues and users.
Desirable Skills
- Theoretical and practical experience in tissue clearing, refractive-index matching and imaging of large cleared specimens.
- Experience in multiphoton/non-linear microscopy, live-cell imaging, advanced super-resolution or single-molecule imaging.
- Experience with machine learning/deep learning for bioimage analysis, including model application, validation and/or development.
- Experience with optical development, custom-built microscopy, alignment, calibration or integration of optical and optomechanical components.
- Experience with image registration, stitching, 3D reconstruction, large-data workflows and reproducible analysis pipelines.
- Teaching, workshop facilitation or formal user-training experience.
- Previous experience in a core facility, shared research infrastructure or other multi-user scientific service environment.
Languages: ENGLISH
Level: Excellent
Additional Information
Benefits
- Competitive remuneration commensurate with qualifications and experience, subject to the applicable Champalimaud Foundation employment framework.
- Work in a multidisciplinary research environment combining neuroscience, cancer research, clinical translation, engineering, computation and advanced imaging.
- Hands-on access to state-of-the-art microscopy and image-analysis technologies, with opportunities for continuous professional development.
- Participation in national and international bioimaging networks and exposure to external-access, training and collaborative activities associated with PPBI and Euro-BioImaging.
- Opportunities to contribute to technology-development projects, advanced courses and collaborations with academic and industry partners when compatible with the platform service mission.
- A team culture centred on scientific rigor, user independence, open communication, continuous improvement and shared responsibility for high-quality service.
Remuneration: EUR 2,200 net/month
Initial duration: 48 months, with possibility of renewal, subject to the applicable employment framework and institutional approval.
Eligibility criteria
National, Foreign or Stateless candidate(s) who hold a PhD degree Mathematical, Physical and Natural Sciences or other related scientific areas and a scientific and professional curriculum that reveals a profile appropriate to the activity to be developed.
In case of PhD degrees awarded by foreign higher education institutions, the degree must comply with the provisions of Decree-Law No. 341/2007, of 12th of October, and all formalities established therein must be fulfilled by the deadline for application submission.
Selection process
Candidates will be screened to determine eligibility based on minimum qualifications listed in call.
Candidates meeting minimum requirements will be scored according to the required application materials: CV 50% weighting, motivation letter 25%, interview 25% (only for top three selected candidates).
If provided, and if shortlisted, candidates’ referees may be contacted and reference letters may count towards evaluation.
First-round results (planned): 9 October 2026
Interviews (planned): 12-16 October 2026, in person or remotely
Evaluation Committee: Davide Accardi; Leopoldo Petreanu/Adriana Sanchez-Danes; Pedro Garcia da Silva
Application materials
- Curriculum vitae
- Motivation letter
- Contact details for two professional references
The CV, motivation letter and reference details should be submitted as a single PDF document. Proof of qualifications may be requested at a later stage for formalization of the appointment.
Degrees obtained abroad may need to be formally recognized in Portugal.
How to apply
Candidates must complete the standard application form and submit a single annexed PDF document containing the application materials stated in the call.
The call reference will be asked and not having may invalidate your submission. This call reference is: Microscopist and Imaging Specialist _ ABBE Platform
Applications are also accepted in paper, sent or handed to the Fellows Support Office at the Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal.
Notification of results
All candidates will receive a receipt of acknowledgment within 7-10 business days. The three highest scoring candidates will be notified by email or telephone. All other candidates will be notified solely by email of the final outcome of the recruitment process.
After being notified, candidates will have 10 working days to present a claim for re-address by email ([contact details available in the full listing]). If no claim is received by the Champalimaud Foundation, the Evaluation Committee`s decision will become definitive.
Additional comments
About Us
Research is at the heart of the Champalimaud Centre for the Unknown, a modern research and clinical facility situated on the waterfront in Lisbon, Portugal. The goal of Champalimaud Research (CR) is to perform world-leading fundamental and translational research. Current research work is focused on the fields of neuroscience, physiology and cancer. CR comprises a team of over 400 scientists from around the world. English is the official language of the Centre. Lisbon’s sunny Atlantic Mediterranean climate, vibrant culture and high quality of life make this a great place to live and work.
Relevant Institutional Information
In line with our community guidelines and Equality, Diversity and Inclusion policy and Gender Equality Plan, no candidate may be privileged, favored, prejudiced or deprived of any right or excluded from any duty on the basis of age, sex, gender identity, sexual orientation, race/ethnicity, disability, chronic illness, language, nationality, territory of origin, family status (marital, pregnancy and maternity, having or not having dependents), socioeconomic situation, education, religion, political or ideological beliefs, trade union membership, or on any other grounds which are irrelevant to decision-making.
Legal Notices
The present call has the sole purpose of filling the indicated research position. This call may be canceled at any time on or before the jury’s evaluation of all eligible candidates and the recruitment process shall be concluded on the day of the full execution of the contract between the Champalimaud Foundation and the selected candidate.
Work Location(s)
Number of offers available: 1
Company/Institute: Champalimaud Fundation
Country: Portugal
Contact
City: Lisboa
Website: https://fchampalimaud.org/champalimaud-research
Street: Champalimaud Centre for the Unknown
Postal Code: 1400-038
