Microscopist and Imaging Specialist (PhD level)

Fundação Champalimaud; Lisboa; Presencial; EUR 21 000 - 28 000; Tempo integral

Resumo da oferta

The Champalimaud Foundation in Lisbon, Portugal, seeks a Microscopist and Imaging Specialist (PhD level) to join the ABBE Platform within Champalimaud Research. You will provide expert microscopy planning, acquisition guidance and first-line image analysis support across confocal, super-resolution and light-sheet modalities.

As part of a multi-user facility, you will train users, optimize workflows, coordinate with platform colleagues, and contribute to technology development while maintaining

Qualificações

• PhD in Biology, Physics, Engineering, Biophysics, or related field.
• Solid hands-on experience in advanced light microscopy and understanding of image formation, resolution, sampling, SNR and phototoxicity.
• Fluency in English, the working language of Champalimaud Research.

Responsabilidades

• Provide scientific consultation for imaging projects with robust microscopy strategies and controls.
• Train users in basic and advanced light microscopy with one-to-one sessions and courses.
• Provide expert support in confocal, super-resolution, deep-tissue, light-sheet, widefield imaging and automated slide scanning.
• Support imaging of living and fixed samples, advising on phototoxicity and optical issues.
• Provide first-line image visualization, 3D reconstruction and quantification using Fiji/ImageJ and related tools.
• Perform routine instrument checks, maintenance and troubleshooting, coordinating with manufacturers as needed.
• Contribute to implementation and optimization of new imaging technologies and workflows.
• Coordinate with other institutional platforms for integrated workflows.
• Support external-access projects and collaborations under PPBI/Euro-BioImaging.

Conhecimentos

Fluency in English

Service orientation

Communication

Training

Independent work

Python/C/C++ programming

Programming concepts

Formação académica

PhD in Biology/Physics/Engineering/Biophysics or related

Ferramentas

IMARIS CF

Arivis

Aivia

Fiji/ImageJ

Descrição da oferta de emprego

Microscopist and Imaging Specialist (PhD level)

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.

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

Requirements

Research Field: Technology
Education Level: PhD or equivalent

Skills / Qualifications

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.

Essential Qualifications

• 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 that will also be considered

• 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

• 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

Application materials

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.

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 ([e-mail] ). If no claim is received by the Champalimaud Foundation, the Evaluation Committee`s decision will become definitive.

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.

Additional 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.