Mots-Clés

image analysis, spatial, segmentation, single-cell

Description

Institut Curie Research Center

Institut Curie is a major player in the research and fight against cancer. It consists of a Hospital group and a Research Center of more than 1000 employees with a strong international representativeness. The objective of the Research Center is to develop basic research and to use the knowledge produced to improve the diagnosis, prognosis, and therapeutics of cancers as part of the continuum between basic research and innovation serving the patient.

Laboratory

The bioinformatics core facility of Institut Curie (https://curie.fr/plateforme/curiecoretech-bioinformatique-cubic) is composed of more than 20 bioinformaticians with skills ranging from high-performance computing and data management to bioinformatics and statistical data analysis. In 2020, 4 core facilities of the institute (Custom Single Cell Omics, NGS, Cytometry and Bioinformatics platforms) joined their forces to create the Single-cell Initiative in order to maximize services and development of single-cell omics for the scientific community.

Recently, the Single-cell Initiative (https://curie.fr/plateforme/initiative-single-cell) has initiated exciting new projects related to spatial data analysis using either high-resolution whole-slide fluorescence imaging (Orion system) or spatial transcriptomics approaches (10X Visium system). These promising technologies combine visual/spatial information with large-scale molecular information and thus represent a great challenge in terms of data analysis and integration.

The project

The candidate will work in a stimulating multidisciplinary environment composed of the bioinformatics core facility and the single-cell initiative, in close collaboration with the cell and tissue imaging facility. The candidate will be in charge of highly diverse projects, ranging from testing and designing image analysis workflows supporting new technologies and developing custom tools, to full collaborations with biologists to analyse spatial omics data.

The candidate will participate to :

• Testing, implementing and deploying tools for image/spatial analysis and processing (stitching, segmentation, quantification, cell clustering analysis)

• Building custom analysis tools/pipelines for projects requiring specific developments.

• Work with scientists for writing / implementing algorithms to solve image processing problems from multidimensional microscopy datasets.

• Improve existing tools (computing speed, user interface, creating workflow).

• Validation of developed tools.

• Train scientists in the use of developed tools and make tutorials.

Training and Skills required

The candidate should hold an engineering or master’s degree in bioinformatics, (bio)physics, applied mathematics or any other related domain, followed by a first professional experience in bioinformatics or bioimage analysis or holds a PhD in bioimage analysis, bioinformatics, (bio)physics, applied mathematics or any other related domain.

Skills required :

• Applied mathematics or data science with knowledge in Image Analysis

• Experience with Image format (OME-TIFF), processing, data visualization and pipeline development (stitching, segmentation, quantification)

• Programming skills (e.g. Python, R)

• An experience with biology, single-cell sequencing and imaging is advantageous

• Able to collaborate with others on their projects and to work in teams

• Able to communicate in English