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

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.

Several postdoctoral positions are opened at the Institut Pasteur (Paris, France) to visualize the topological and functional dynamics of small regulatory pieces of DNA, called enhancers, in the animal genome. Successful candidates will join a collaborative and interdisciplinary venture in the newly formed unit Physics of Biological Function of biophysicist Thomas Gregor.

Presentation of the unit and its research topics:

The Unit for the Physics of Biological Function at Institut Pasteur studies the basic physical principles that govern the existence of multicellular life. A core focus of the lab is to understand biological development–the complex process through which an organism grows from a single cell into a differentiated, multicellular organism–from a physics perspective. As such, we formulate and experimentally validate quantitative models that describe how individual cells interact and organize in order to generate complex life forms. Our main interests lie in:

  • multicellular pattern formation
  • transcriptional regulation in the context of development
  • molecular limits to biochemical sensing
  • emergence of collective behaviors in multicellular system
Description of a representative project:

The dynamic organization of the genome in time and space plays a crucial role in the functional specification of a cell. In particular the interplay between multiple distant enhancers and their target gene promoters has critical mechanistic consequences on gene activity patterns during cell differentiation and development. We are developing state-of-the- art high-resolution live imaging techniques to resolve multiple enhancers in space and time to correlate the 3D motion of the DNA polymer with gene activity. The challenge is to develop the right imaging modalities that optimize our need for high temporal and spatial resolution, and to image a large field of view with multiple (≥ 4) colors simultaneously. [For more information see: Chen et al. (2016). Direct visualization of transcriptional activation by physical enhancer-promoter proximity. bioRxiv 099523; doi: https://doi.org/10.1101/099523.]

Expected profile of the candidate:

Candidates will have a strong interest for collaborative and interdisciplinary research. They should have a proven successful track record equipped with a combination of the following skills:

  • live-cell microscopy, single molecule imaging
  • microscope design and implementation
  • hard- and software design for microscope control
  • computational image analysis

Ability to work independently and in collaboration with members of the lab and international collaborators in a dynamic, diverse and multinational group is essential. English is the working language.

Contact: thomas.gregor@pasteur.fr Applications should include a statement of research interests and motivation, a CV, and contact information for three references. Applications will be reviewed as soon as they are received. Funding is available for multiple positions but candidates will be encouraged to apply for independent competitive grants. Long-term funding is possible upon mutual agreement. Alternative projects that match with the overall goals of the unit can be discussed at the interview stage.

The newly founded unit Physics of Biological Function of biophysicist Thomas Gregor at Institut Pasteur is seeking to fill two open position at the engineer level to perform microscopy and imaging related research. Candidates with strong interest in interdisciplinary optical microscopy and biophysics research will be expected to build microscopes, run live imaging experiments and execute image processing and analysis routines.

Presentation of the unit and its research topics:

The Unit for the Physics of Biological Function at Institut Pasteur studies the basic physical principles that govern the existence of multicellular life. A core focus of the lab is to understand biological development–the complex process through which an organism grows from a single cell into a differentiated, multicellular organism–from a physics perspective. As such, we formulate and experimentally validate quantitative models that describe how individual cells interact and organize in order to generate complex life forms. Our main interests lie in:

  • multicellular pattern formation
  • transcriptional regulation in the context of development
  • molecular limits to biochemical sensing
  • emergence of collective behaviors in multicellular system
Description of a representative project:

The dynamic organization of the genome in time and space plays a crucial role in the functional specification of a cell. In particular the interplay between multiple distant enhancers and their target gene promoters has critical mechanistic consequences on gene activity patterns during cell differentiation and development. We are developing state-of-the- art high-resolution live imaging techniques to resolve multiple enhancers in space and time to correlate the 3D motion of the DNA polymer with gene activity. The challenge is to develop the right imaging modalities that optimize our need for high temporal and spatial resolution, and to image a large field of view with multiple (≥ 4) colors simultaneously.

Expected profile of the candidate:

Candidates will have a strong interest for collaborative and interdisciplinary research. They should have a proven successful track record equipped with a combination of the following skills:

  • live-cell microscopy, single molecule imaging
  • microscope design and implementation
  • hard- and software design for microscope control
  • computational image analysis

Ability to work independently and in collaboration with members of the lab and international collaborators in a dynamic, diverse and multinational group is essential. English is the working language.

Contact: thomas.gregor@pasteur.fr Applications should include a statement of research interests and motivation, a CV, and contact information for three references. Applications will be reviewed as soon as they are received. Funding is available for multiple positions; long-term funding is possible upon mutual agreement.

To identify genes regulating the assembly and the disassembly of RNA/protein complexes, the group of F. Besse (iBV, Nice) has started a genome-wide screen relying on high throughput imaging of cultured cells. The goal of this screen is to identify mutant conditions in which the properties (number, size, distribution…) of RNA/protein particles labeled with a fluorescent protein are altered. Automatic image analysis methods are required to quantitatively and statistically analyze the millions of images generated by the screen, and to identify classes of mutants.

The candidate will develop a statistical and classification framework to identify and characterize different populations of genes having an impact on the population of RNA/protein particles. This includes (i) the definition of a diffeomorphism that maps any individual cell into a common space (mean shape or model), (ii) the definition of a spatial statistical framework to define a notion of configuration of particles as an additional characterization of a cell (mean configuration, covariance), and (iii) the development of an unsupervised classification scheme.

The candidate will work under the supervision of Xavier Descombes and Eric Debreuve (Centre INRIA Sophia Antipolis/I3S; http://www-sop.inria.fr/morpheme/), in close collaboration with biologists from F. Besse’s team (Fabienne de Graeve and Florence Besse). The position is funded for 12 months and should start on the 1st of March 2018 at the latest.

Read more: click “Download complete presentation” at the top of the page.

Impact of the tissue properties in epithelial morphogenesis

In monolayered epithelia, differentiated cells display a specific apico-basal organization. To maintain cell polarization and cohesion of neighbouring cells, cells developed diverse adhesion complexes. However, the epithelial monolayer is subjected to remodelling during organism development or tissue repair. In addition, cell renewal, cell rearrangements and cell extrusion occur to maintain the monolayer homeostasis. Consequently, the epithelium has to constantly maintain its apico-basal compartimentation and to collectively adapt to its microenvironment to maintain its polarized and cohesive state. Based on the recent development of a biomimetic 3D culture system in our lab (Nature Communications, 8 :13998), we study the impact of the physical properties of the microenvironment on epithelial behaviour and global tissue morphogenesis, and to determine the regulatory mechanisms.

We are seeking to recruit a post-doctoral researcher with background in cell/developmental biology, biophysics, and/or bioengineering. The postdoc will benefit from an interdisciplinary environment with expertise in cell biology, biochemistry, developmental biology and imaging, and will have access to leading edge equipment.

Requirements :

  • PhD in cell/developmental biology or in biophysics
  • High degree of motivation and strong interest towards interdisciplinary work
  • Good level in image analysis (ImageJ, Matlab)
  • Skills in confocal and/or biphoton microscopy and live imaging.

Starting date: Summer/Fall 2017. The date indicated above is not firm.
Deadline for application: open until filled.