Image Analysis and Data Management Expert 100%, Basel, permanent
ETH Zürich
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Image Analysis and Data Management Expert
100%, Basel, permanent
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ETH Zurich is a world-leading university dedicated to advancing science, engineering, and technology. The Single Cell
Facility (SCF) is a central research and service platform at the Department of Biosystems Science and Engineering
(D-BSSE) of the ETH with location in Basel. It is a departmental core facility providing access to a high-end
instrument portfolio for optical single cell analysis such with light microscopy and flow cytometry technology. The SCF
is part of the D-BSSE's commitment to elucidate the design principles of cells in stochastic environments and their
exploitation for network design. The SCF staff works closely with the Lab Automation Facility (LAF) team, which
develops and maintains complex robotic setups integrated with readout technologies such as high content imaging for
experimental workflows in biology and biochemistry.
Project background
The SCF's centralized instrument pool is accompanied by expert service provided by staff who offer instrument
training, hardware and software maintenance, and advice on sample preparation, assay design, image analysis, and data
management.
As a member of the SCF, you will perform image analysis, data management, and other IT-related projects for SCF users
and staff related to a wide variety of biology and biotechnology projects. Starting date: 1. June 2025.
Job description
As a member of the SCF, you will perform image analysis on microscopy data, data management for various applications
and pipelines of the facility, and other IT-related projects for SCF users and staff related to a wide variety of
biology and biotechnology projects.
Your resposibilities:
- First line support for image analysis requests (from optical microscopy).
- Providing expert input to microscopy imaging projects to help design experimental protocols in close collaboration
with SCF microscopy experts to align analysis strategies with image acquisition parameters.
- Train users in the use of existing analysis software (Imaris, Huygens, Fiji, ImageJ, CellProfiler, MATLAB, etc.).
Keep abreast of developments in such commercial and open-source image analysis tools.
- Develop ad-hoc solutions for specific user projects (MATLAB scripts, ImageJ macros/plug-ins, CellProfiler pipelines,
Python coding, etc.).
- Organization and teaching of an image analysis module in a laboratory course for biotechnology master students.
- Development of analysis software tools for proprietary image formats (super-resolution data, plug-ins).
- Contribute to the creation and maintenance of the infrastructure (hardware and software) of the facility:
- Content creation and maintenance of the facility's website and wiki management.
- Maintenance of the facility's resource and booking management tool (openIRIS).
- Development of tools for the maintenance of the analysis and acquisition machines (data movers, data pipelines,
storage management).
- Scouting for new commercial and open-source software tools.
- Develop image analysis-based quality control tools for microscopes.
Profile
We are looking for an enthusiastic, service-oriented, proactive personality with great team spirit and drive to
collaborate with others on their projects within a scientific core facility.
- PhD in natural sciences, preferably with a strong background in life sciences (cell and molecular biology,
biotechnology).
- Familiarity with microscopy experimental workflows and data from different types of instruments (automated/smart,
confocal, super-resolution, light sheet microscopy).
- Knowledge of state-of-the-art image processing and analysis tools and a track record in developing innovative image
analysis and data science tools.
- Adept in software engineering with fluency in programming languages such as MATLAB, C++, C#, Java, Python (Napari,
Stardist, Scikit-image), PHP, SQL, Tcl/Tk.).
- Knowledge of training and/or application of deep learning models.
- Experience with data pipelines following FAIR principles, with skills in compressed sensing, image noise reduction
and big data management, cloud computing, high performance computing, virtual machine infrastructure.
- Use and administration of various operating systems.
- Self-motivated and able to work both independently and in a team.
- Experience of working in a multidisciplinary environment and ability to manage several projects simultaneously with
a high degree of technical autonomy.
- Superior communication skills in written and spoken English.
Workplace
Workplace
We offer
- A stimulating work environment with state-of-the-art facilities and technology portfolio at one of the world’s top
universities
- Work in an international and multidisciplinary team embedded in a vibrant research community
- Benefits. competitive salary and excellent benefits in accordance with ETH Zurich guidelines
chevron_right Working, teaching and research at ETH Zurich
We value diversity
In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value
diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students
are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open
environment that allows everyone to grow and flourish.
Curious? So are we.
We look forward to receiving your online application with the following documents:
- Cover letter describing your motivation to apply for this position.
- Detailed curriculum vitae with references and their contact details.
- Please provide us with links to your software samples (e.g. Github) with clear indications of your contributions.
Please note that we exclusively accept applications submitted through our online application portal. Applications via
email or postal services will not be considered.
Further information about the SCF and LAF can be found on our websites. Questions regarding the position should be
directed to Dr. Thomas Horn email thomas.horn@bsse.ethz.ch (no applications).
For recruitment services the GTC of ETH Zurich apply.
About ETH Zürich
ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.
About ETH Zürich
ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.
100%, Basel, permanent
print Drucken
ETH Zurich is a world-leading university dedicated to advancing science, engineering, and technology. The Single Cell
Facility (SCF) is a central research and service platform at the Department of Biosystems Science and Engineering
(D-BSSE) of the ETH with location in Basel. It is a departmental core facility providing access to a high-end
instrument portfolio for optical single cell analysis such with light microscopy and flow cytometry technology. The SCF
is part of the D-BSSE's commitment to elucidate the design principles of cells in stochastic environments and their
exploitation for network design. The SCF staff works closely with the Lab Automation Facility (LAF) team, which
develops and maintains complex robotic setups integrated with readout technologies such as high content imaging for
experimental workflows in biology and biochemistry.
Project background
The SCF's centralized instrument pool is accompanied by expert service provided by staff who offer instrument
training, hardware and software maintenance, and advice on sample preparation, assay design, image analysis, and data
management.
As a member of the SCF, you will perform image analysis, data management, and other IT-related projects for SCF users
and staff related to a wide variety of biology and biotechnology projects. Starting date: 1. June 2025.
Job description
As a member of the SCF, you will perform image analysis on microscopy data, data management for various applications
and pipelines of the facility, and other IT-related projects for SCF users and staff related to a wide variety of
biology and biotechnology projects.
Your resposibilities:
- First line support for image analysis requests (from optical microscopy).
- Providing expert input to microscopy imaging projects to help design experimental protocols in close collaboration
with SCF microscopy experts to align analysis strategies with image acquisition parameters.
- Train users in the use of existing analysis software (Imaris, Huygens, Fiji, ImageJ, CellProfiler, MATLAB, etc.).
Keep abreast of developments in such commercial and open-source image analysis tools.
- Develop ad-hoc solutions for specific user projects (MATLAB scripts, ImageJ macros/plug-ins, CellProfiler pipelines,
Python coding, etc.).
- Organization and teaching of an image analysis module in a laboratory course for biotechnology master students.
- Development of analysis software tools for proprietary image formats (super-resolution data, plug-ins).
- Contribute to the creation and maintenance of the infrastructure (hardware and software) of the facility:
- Content creation and maintenance of the facility's website and wiki management.
- Maintenance of the facility's resource and booking management tool (openIRIS).
- Development of tools for the maintenance of the analysis and acquisition machines (data movers, data pipelines,
storage management).
- Scouting for new commercial and open-source software tools.
- Develop image analysis-based quality control tools for microscopes.
Profile
We are looking for an enthusiastic, service-oriented, proactive personality with great team spirit and drive to
collaborate with others on their projects within a scientific core facility.
- PhD in natural sciences, preferably with a strong background in life sciences (cell and molecular biology,
biotechnology).
- Familiarity with microscopy experimental workflows and data from different types of instruments (automated/smart,
confocal, super-resolution, light sheet microscopy).
- Knowledge of state-of-the-art image processing and analysis tools and a track record in developing innovative image
analysis and data science tools.
- Adept in software engineering with fluency in programming languages such as MATLAB, C++, C#, Java, Python (Napari,
Stardist, Scikit-image), PHP, SQL, Tcl/Tk.).
- Knowledge of training and/or application of deep learning models.
- Experience with data pipelines following FAIR principles, with skills in compressed sensing, image noise reduction
and big data management, cloud computing, high performance computing, virtual machine infrastructure.
- Use and administration of various operating systems.
- Self-motivated and able to work both independently and in a team.
- Experience of working in a multidisciplinary environment and ability to manage several projects simultaneously with
a high degree of technical autonomy.
- Superior communication skills in written and spoken English.
Workplace
Workplace
We offer
- A stimulating work environment with state-of-the-art facilities and technology portfolio at one of the world’s top
universities
- Work in an international and multidisciplinary team embedded in a vibrant research community
- Benefits. competitive salary and excellent benefits in accordance with ETH Zurich guidelines
chevron_right Working, teaching and research at ETH Zurich
We value diversity
In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value
diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students
are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open
environment that allows everyone to grow and flourish.
Curious? So are we.
We look forward to receiving your online application with the following documents:
- Cover letter describing your motivation to apply for this position.
- Detailed curriculum vitae with references and their contact details.
- Please provide us with links to your software samples (e.g. Github) with clear indications of your contributions.
Please note that we exclusively accept applications submitted through our online application portal. Applications via
email or postal services will not be considered.
Further information about the SCF and LAF can be found on our websites. Questions regarding the position should be
directed to Dr. Thomas Horn email thomas.horn@bsse.ethz.ch (no applications).
For recruitment services the GTC of ETH Zurich apply.
About ETH Zürich
ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.
About ETH Zürich
ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our
excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000
people from more than 120 countries find our university to be a place that promotes independent thinking and an
environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we
work together to develop solutions for the global challenges of today and tomorrow.