Job offer data scientist – image data processing  

Turing Centre for Living Systems 

The Turing Centre for Living Systems (CENTURI) is a large, interdisciplinary and interactive research project at  Aix-Marseille University, uniting a growing community of biologists, physicists, mathematicians, computer  scientists and engineers. The aim of the project is to decipher the complexity of biological systems through  the understanding of how biological function emerges from the organization and dynamics of living systems. 

CENTURI is seeking a highly motivated research engineer on image data processing to fill the post of data  scientist, within CENTURI’s technology transfer platform. This position will be a central point of data analysis,  data sharing and code sharing for our research community. 

Job duties include, but are not restricted to: 

– Provide advice and support to researchers with image processing and data mining (large data analysis  and integration, unsupervised/supervised learning, dimension reduction, statistics, deep learning  techniques, etc.) 

– Assist in transfer of knowledge between the teams of the CENTURIproject 

– Have a theoretical understanding of the algorithms used for data analysis; perform independent  literature search to keep abreast of appropriate methods and technologies. 

– Organize and conduct courses on data analysis for the CENTURI community: PhD students, postdocs,  researchers 

– Participate in the setup of an infrastructure for data sharing within the CENTURIproject – Participate in the development and maintenance the infrastructure of software sharing and code  transfer within the CENTURI project 

Image data processing will be at the core of the project. The successful candidate will be part of the data lab  team of the CENTURI engineering platform. Your expertise will help shape the data sharing and analysis  platform and you will be able to learn from, as well as share your knowledge within the CENTURI community. You will also interact with other engineering platforms on the Luminy campus.  

Your qualifications / expected profile 

You have a Master’s degree (at least) or a PhD (preferred) in data science (University, engineering school),  Computer Sciences or in Physics/Engineering/Applied Physics, with a strong interest and experience in  computational developments together with knowledge of image processing and analysis, statistical data  modelling and analysis (including multimodal data), signal filtering. Experience in machine learning theory  and practice would be a strong asset.

You have a strong experience (at least 5 years with a Master’s degree, at least three years with a PhD) in  research support or research in biological data analysis. Experience in a service facility is strongly  advantageous. Teaching experience would be a plus. 

Experience in professional software engineering and development, as well as data analysis and data sharing  strategies are beneficial. Ideally, the candidate will be familiar with common programming languages,  including Python, Java, C/C++, as well as proficient in a statistical analysis software, such as R or MatLab. In  addition, the candidate will have experience with neural networks training and/or experience in tracking  algorithms.  

You will have strong team-playing abilities and be able to interact with researchersfrommany fields, including  biology, physics, mathematics, and computer science. A friendly, outgoing personality and excellent  communication skills are required, as is the ability to work independently. 

The working language of CENTURI is English, but proficiency in French is beneficial.

What we offer 

CENTURI offers a vibrant, highly interactive working environment with the ability to work with researchers  and engineers from many disciplines. 

CENTURI offers a two-year contract from Aix-Marseille University (renewable). The salary will be based on Aix Marseille University’s salary scale, with a gross monthly salary between €1880 and €3560 (depending on profile  and experience). 

If you are interested, please apply online at the following address:  

http://centuri-livingsystems.org/recruitment/ 

Expected start date: from January 2023 

Application deadline: once the vacancy is filled 

Applications should include: 

– A CV, including a list of publications 

– A cover letter, describing your past experience with data analysis 

– Two recommendation letters

France-Biomaging is looking for a bioimage analyst

Join our efforts to create an open data ecosystem for biological imaging!

One year renewable contract – 2100 – 2358 euros/months gross salary, depending on experience, long term perspectives

Goals

• Build open data collections of microscopy images for deep learning challenges.

• Favor data reuse in the bio-image community.

• Connect biologists and image analysis experts.

Main activities

• Identify, define, expose key challenges in bioimage analysis.

• Recruit and encourage researchers to share their images using FAIR principles

• Organize R&D competitions (see kaggle data science bowl 2018 for an example) that use the created data collections and mobilize the international community: communicate (newsletter, website, Twitter, etc.), define the rules of the competitions, develop IT tools, organize the event, identify and evaluate the results.

• Monitor similar initiatives in the national and international community, particularly in Europe.

• Exchange with the international open microscopy community.

Skills

• Experience in data and metadata management, data stewardship, data engineering.

• Excellent communication skills.

• Experience in frontend development is a plus.

• Programming languages : knowledge of Python, javascript is a plus.

• Experience with biological data is a plus.

Training

Master degree in data science and engineering, computer science, applied mathematics, physics, bioinformatics. Additional training in biology is preferable but not obligatory.

Context

France-BioImaging is a distributed research infrastructure that works at the crossroads of molecular and cellular biology, microscopy, engineering and computer science. This unique infrastructure brings together major imaging facilities and research teams performing R&D in bioimaging across France.

The DATA project brings together 7 engineers to bring about transformative changes in data management and analysis within the bioimage community. Key outputs expected from this project include the deployment of cloud-based image repositories obtained with high throughput imaging techniques and the development of efficient deep learning workflows feeding from these data.

The engineer will be hosted at the Insitut Pasteur in Paris and will benefit from the direct supervision of leading experts Drs. C. Zimmer (Institut Pasteur) and T. Walter (École des Mines).

Please send a CV and motivation letter to edouard.bertrand@france-bioimaging.org

Goal

Participate in the “DATA” project of the France-BioImaging infrastructure, which is dedicated to biological imaging (see https://france-bioimaging.org/). The goal of the work will be to create annotated image databases suitable for machine learning and to set up R&D competitions to solve bottlenecks in bioimage analysis.

Main activities

  • Participate in the identification of key questions in bioimage analysis.
  • Deploy and configure image database management systems (OMERO by default) and develop tools to facilitate manual image annotation.
  • Mobilize the community of image producers to contribute to this database.
  • Organize R&D competitions that use these databases and that mobilize the international community: communicate (newsletter, website, Twitter, etc.), define the course of the competitions, develop their IT tools, organize the event, identify and evaluate the participant results.
  • Monitor similar initiatives in the national and international community, particularly in Europe.

Expected skills

  • Experience in programming.
  • Experience in machine learning and evaluation of its methods.
  • Experience with competitions is a plus.
  • Experience in image analysis and some of its basic software tools (e.g. Image J/FiJi, Icy, Ilastik, ImJoy …) is a plus.
  • Knowledge of at least one image data management software (eg OMERO) or client server architectures.

Diplomas

  • Master in computer science, applied mathematics, physics, bioinformatics or related field; dual biology/computational science skills preferable but not obligatory.

Context

France-BioImaging is a distributed research infrastructure that works at the crossroads of molecular and cellular biology, biophysics, engineering, mathematics and computer science.
This unique infrastructure brings together major imaging facilities and research teams performing R&D in the bioimaging field. The infrastructure aims at developing new image analysis tools based on deep learning. For this, the engineer will work with a team of ~10 people that will implement the France-BioImaging “DATA” project. The engineer will be located in Paris and will be under the direct supervision of Drs. C. Zimmer (Pasteur) and T.
Walter (Ecole des Mines).

Application deadline: 15th JUNE 2022

Send your CV and motivation letter to edouard.bertrand@france-bioimaging.org

Bioimage Analyst Position

The imaging core facility Montpellier Ressources Imagerie (MRI) offers equipment (84 instruments) and expertise (32 people) in the fields of light microscopy, flow cytometry, X-ray tomography and high-throughput imaging. It is used by approximately 850 users every year. MRI is part of the Biocampus Montpellier Unit (UAR 3426 CNRS, US 9 INSERM) and a member of the France BioImaging infrastructure. 

The facility is seeking to hire a contract engineer to expand its image analysis service. The selected engineer will join a small team of analysts,  working in close cooperation with the facility’s biologists and microscopists.

  • Mission

The main mission of the engineer is to participate in the project-based creation of automated image analysis tools. He will also guide and advise facility users in matters of image analysis, and promote the use of best practices in biological image analysis.

  • Activities

  • Design and implement tools for automated image analysis and processing using ImageJ/Fiji, java, python and other platforms.
  • Set-up advanced workflows, including:  image segmentation, quantification of intracellular protein distribution, pattern recognition, tracking of dynamic particles
  • Train and integrate deep-learning methods into image analysis workflows
  • Work with scientists to write and implement algorithms for solving image processing problems from multidimensional fluorescence microscopy datasets.

  • Associated Activities

  • Train scientists in the use of developed tools and make tutorials
  • Participate in project meetings
  • Maintain, list and promote already existing tools
  • Communicate about developed tools at scientific conferences or in scientific journals

  • Expected Knowledge and skills

  • A solid training in programming and software engineering.
  • Knowledge of biological image analysis methods and tools.
  • While no formal biology training is needed, a strong interest in biology would facilitate the interaction with biologist users.
  • Ability to work in a team and have an interest in multidisciplinary approaches
  • French and English communication skills.

Required degree: Master degree in computer science, (bio) physics, applied mathematics, bio-image analysis or a related field

Recruitment from 1.09.2021, Type of contract: Fixed-term contract – 12 months (renewable) 

Please apply at https://bit.ly/2RU5gKE

 

A postdoc position is available as part of an international HFSP funded collaboration in the group of Rafael Carazo Salas, University of Bristol UK, from 1 September 2019 (https://research-information.bristol.ac.uk/en/persons/rafael-e-carazo-salas(a7638b29-53e4-49ba-82b5-98b21d82f41f).html).

Making personalised stem cell therapeutics a reality will require that we understand how to predictively engineer in vitro replacement cells and tissues robustly and in a tumour-free manner, on a person-by-person basis.

Towards that goal the Carazo Salas group is establishing innovative experimental and computational tools and pipelines combined with human pluripotent stem cell technologies (hESC, hiPSC), to elucidate the quantitative & mechanistic basis of efficiency, specificity & tumourigenic potential in human pluripotent stem cell differentiation and identify ways to improve personalised tissue engineering.

As part of that we have recently established large-scale, multiday, multicolour time-lapse microscopy pipelines allowing us to follow at single-cell level how ‘live’ human stem cells proliferate and differentiate over time, to better understand why some cells become efficiently programmed into intended target cell types and others do not. In practice this means we routinely image thousands of ‘live’ human stem cells in multiple epifluorescence microscopy channels (to monitor multiple live reporters of their proliferation and fate) every 10 minutes through multiple days, which gives rise to millions of single-cell data points in feature space from which we want to derive predictive information about cell fate.

We are looking to hire a highly motivated and talented computational postdoc with prior expertise in quantitative image analysis (particularly in cell segmentation and tracking from multi-channel time-lapse fluorescence microscopy images) and machine learning (particularly novel approaches like CNNs, GANs) to help us extract from those images information enabling us to understand and predict why each cell makes the fate decision it makes.

The selected computational scientist will work on a daily basis in close collaboration with experimentalists, and also as part of a larger collaboration with groups in Switzerland and the USA.

Applicants interested in this post should hold a PhD in Computational Image Processing, Computer Vision, Machine Learning or a related subject, have an excellent track record and extensive experience with computational image analysis and/or machine learning, and be excited to work in an interdisciplinary environment. Experience working with timelapse microscopy imaging of cells or high-throughput/high-content microscopy is a plus.

For enquiries, please contact Rafael E. Carazo Salas at rc16805@bristol.ac.uk and if you’re not that person please spread the word to somebody who might.

Nature careers ad is found here: https://www.nature.com/naturecareers/job/research-associate-computational-postdoc-university-of-bristol-uob-692681.

About

The Image Analysis Hub is an open access, equal access core facility committed to offering support in image analysis. Our webpage is: https://research.pasteur.fr/en/team/image-analysis-hub/

What we do.

As part of the C2RT, we strive to ensure the continuity between image acquisition and image analysis. To this end we rely on our expertise in imaging and collaborate with other facilities such as the UTechS-PBI and UTechS-UBI when pertinent. All requests involving images are considered.

 

Our services follow four axes:

1. Offer walk-in support and trainings for questions involving image analysis.

This activity aims at offering to users quick answers to scientific questions involving well-established pipelines, for which a commercial or published tool exists and can be used conveniently. Users can address their question to the facility during open-desk sessions or directly via one-to-one requests. Depending on the effort involved, the solution is derived and proposed onsite, or individual  trainings are scheduled. For general topics, the Hub organises regular courses and workshops, possibly involving external teachers or providers.

For instance, see below for the announcement of our open-desk, organised regularly every two week.

 

2. Build and deploy custom analysis tools for projects requiring special developments.

Research endeavours to address original questions, for which analysis tools might be lacking or incomplete. The Image Analysis Hub aims at creating or implementing novel tools based on existing algorithms to address these questions, using skills in image analysis and software development. More than just developing the analysis tool, this activity often involves deriving a suitable analysis methodology, for which the facility expertise in microscopy and biophysics is key. Engineers work in close collaboration with users within the framework of a scientific project over medium or long durations. For projects whose effort would extend beyond typical facility usage or involve original research work, the project may be directed to the BioImage Analysis unit after a discussion with all parts.

 

3. Maintain an infrastructure for autonomous image analysis. Deal with complex tool deployments.

Data volume and modern analysis techniques may call for a computing power not always present in Pasteur labs. Providing open-access workstations unlock barriers to compute-intensive tools. They also act as the central sharing points for commercial softwares, making them available to the whole campus. Finally, some specialized tools require special deployment efforts, e.g. to make such a tool able to exploit the HPC infrastructure of the Institut Pasteur.

 

4. Develop original and innovative software tools for image analysis, whose scope exceed user projects.

Software development and image analysis skills of the facility can be leveraged to build ambitious software tools shipping innovative technologies. These tools exceed the scope of single projects and address the unarticulated needs of the Pasteur community and their creation is part of the development activity of the facility.

THE ROLE  In this role, you will play a leadership role in supporting the development of new tools and facilitating collaborations in the imaging and microscopy community, especially in the areas of image analysis and visualization for cell biology. Our support of this ecosystem will likely take many forms, including grantmaking to biologists and computational scientists and developing open-source tools among the science community and CZI computational biologists and software engineers. The ideal candidate will have deep, hands-on expertise in quantitative microscopy, and at least some familiarity with the current open-source imaging software ecosystem (e.g. ImageJ, FIJI. CellProfiler, etc.) and core technologies (Python, TensorFlow, WebGL). Key qualities are (1) an understanding of how biologists want to work with imaging data; (2) a passion for community engagement and open-source development; and (3) strong interpersonal skills and ability to build and work across a diversity of expertise.

### RESPONSIBILITIES

  • Work closely with Science Program Officers, Computational Biologists, and Technology Staff to help define and lead programs in imaging and microscopy and represent them to the outside community
  • Collaborate with biologists, imaging scientists, and open-source software developers to help conceive and develop analysis and visualization tools for biological imaging data
  • Drive internal and external community engagement, including planning and running hackathons and meetings, and engage in outreach to ensure connections to users, standards groups, and existing open-source communities
  • Support the grantmaking process for current and future programs, including selection, review, process, and relationship management
  • Identify and engage with existing open-source communities, and help build consensus around standards and methods

### QUALIFICATIONS

  • PhD degree or equivalent experience in quantitative microscopy or similar field
  • 3+ years of experience analyzing microscopy image data, including the use of common open-source tools (e.g. ImageJ, FIJI, CellProfiler) and at least one modern software analysis or visualization ecosystem (e.g. Python, TensorFlow, WebGL, etc.)
  • 3+ years of experience in physical or virtual community-building activities, including hackathon planning, workshop or conference organization, hosting tutorials, etc.
  • 3+ years working in or helping coordinate open-source software communities