Post-doctoral researcher at FIMM

Post-doctoral researcher at FIMM High-Content Imaging and Analysis unit

FIMM High-Content Imaging and Analysis (FIMM-HCA; https://www.fimm.fi/en/services/technology-centre/high-content-imaging-a…) unit is part of HiLIFE-HELMI (Helsinki Advanced Light Microscopy) platform and FIMM Technology Center. We provide service to our academic and commercial customers in high-content/high-throughput microscopy, image analysis and data management. FIMM-HCA is now seeking for a service-oriented post-doctoral researcher to develop and run activities of recently established core unit.

The primary activities of the position include, but are not limited to:
• Run and develop the activities of FIMM-HCA unit including:
• Project management and coordination
• High-throughput microscopy and analysis
• Development of image analysis solutions, methods and protocols
• Maintenance of the microscopes
• Administrative activities of the unit
• Collaboration with FIMM TC, other HELMI partners, and international partners

You will be a member of Peter Horvath’s research group (https://www.fimm.fi/en/research/groups/horvath), which works in close collaboration with Olli Kallioniemi’s research group (https://www.fimm.fi/en/research/groups/kallioniemi) in developing new advanced image analysis methods for biomedical applications. You will have the opportunity to build collaborative network with various academic and commercial partners in international research environment of FIMM. In your daily work, you will utilize our new PerkinElmer Opera Phenix spinning-disk high-content screening microscope, and design and run the follow-up analysis of the imaging data. You will also manage and design projects with commercial partners, and offer training to local users.

The successful candidate should
• Hold a PhD degree (or similar, or graduating soon) in computer science, cell biology or related field
• Have thorough image analysis experience
• Have experience in fluorescence microscopy
• Be technically capable of designing new image analysis pipelines and handle big data
• Be fluent in English, have good interpersonal and communication skills, a service-minded attitude, and be able to work independently as well as within a team
• Have good problem-solving and analytical skills
• Should state if also has proven experience with: project management and coordination, supervision of personnel, drug sensitivity testing, high-content microscopy, laboratory automation, robotics, and high-throughput screening
• The earlier experience on collaboration with companies, and activities in high-throughput microscopy is not essential but beneficial

The salary will be commensurate with qualifications based on the university salary system. A contract will be offered initially until 31.12.2019. Extension beyond this is possible depending on the availability of funding.

Application should be written in English and include a cover letter and CV with contact information for two referees.

Please submit your applications through the University of Helsinki electronic recruitment system by clicking on the Apply link. Internal applicants (i.e., current employees of the University of Helsinki) please submit your applications through the SAP HR portal by September 25, 2017. Election of candidates will commence on September 26, 2017.

For further information please visit our website at http://www.fimm.fi or contact a current unit head Lassi Paavolainen (lassi.paavolainen(at)helsinki.fi), or Vilja Pietiäinen (vilja.pietiainen(at)helsinki.fi).

Apply at latest 25.09.2017

APPLY LINK

https://rekry.helsinki.fi/sap/bc/erecruiting/posting_apply?param=cG9zdF9pbnN0X2d…

DUE DATE

Monday, September 25, 2017

More information at: https://www.helsinki.fi/en/open-positions/post-doctoral-researcher-fimm

Image Analysis Specialist at the ZMBH Light Microscopy Core Facility

University of Heidelberg, Germany

Institute Description
Within the life sciences faculties of the University of Heidelberg, the ZMBH (Zentrum für Molekulare Biologie der Universität Heidelberg) is a center of excellence for both research and higher education in basic and biomedical molecular biology. Our research aims at fundamental questions of molecular and cellular biology at the level of molecules, cells and organisms.

Job Description
The ZMBH Imaging Facility seeks to recruit a highly motivated individual to join its team working in the light microscopy core facility in an academic research environment. The Imaging Facility employs a broad range of imaging technologies, is equipped with state-of-the-art microscopes and has a number of research groups working at the interface of biology and biophysics as well as imaging technology development (e.g. superresolution microscopy). This provides an exciting and unique opportunity to work on image processing and analysis in a multidisciplinary environment with researchers in the life sciences.
Remuneration will be based on qualification and the salary structure of the TV-L (public service tariff scale). The initial contract is limited to 2 years.

Responsibilities Include
• Manage image processing software (ImageJ/Fiji,..).
• Help scientists design and build successful image analysis pipelines and data flows using a variety of open source and commercial software packages (ImageJ macro language, Java, Python, MATLAB).
• Manage a “walk-in” advisory service for scientists to guide them to the correct software and image analysis solution.
• Train staff and graduate students in image analysis techniques through workshops and practical courses.
• Collaborate with researchers by writing/implementing algorithms to solve image processing problems from cell biology microscopy data.
• Manage, test and evaluate image acquisition software of microscope systems.
• Maintain the computer workstations of the ZMBH Imaging Facility.

Essential Requirements
• Proven experience applying and/or developing image analysis tools and applications with ImageJ/Fiji, MATLAB, Java or equivalent programming language.
• A university degree (Master degree or, ideally, a PhD) in Biology, Physics, Computer Science, Mathematics or equivalent qualification (e.g. Electrical Engineering).
• Ability to work in a team.
• Experience in light microscopy is welcome but not required.
• Ability to give courses in image processing and analysis.
• Must be fluent in English and have excellent communication skills both verbal and written. Fairly basic German language skills are needed.

Contact
Please send your CV and relevant documents by email to Dr. Holger Lorenz, h.lorenz@zmbh.uni-heidelberg.de, with the subject “Image Analysis Specialist”. The deadline for applications is August 31, 2017.

ZMBH – Central Services – Imaging Facility – Open Positions

Scientist / IT Engineer – Image Analysis in Light & Electron Microscopy

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton near Cambridge (UK), Monterotondo near Rome (Italy) and Barcelona (Spain).

The Centre for Molecular and Cellular Imaging (CMCI) at the EMBL supports projects on biological imaging at EMBL at different scales of biological organization, from the atom to the organism. The core mission of the Centre is to provide support in image analysis of light and electron microscopy data. Therefore the CMCI is searching for a scientist with strong background in computational image data analysis and extensive experience in applications to biological questions.

The successful candidate will be responsible for the integration of existing and development of new image processing tools to turn biological imaging of cells, tissues and organisms from qualitative descriptions into quantitative measurements and assays. He/she will make software tools accessible to a community of in-house as well as external users, making use of existing software packages where adequate. In addition, the scientist is expected to consult and train EMBL and visiting scientists on the usage of image analysis tools. He/she will be strongly involved in the organisation and teaching of in-house and international courses on basic and advanced image analysis and data management.

Qualifications and Experience

The candidate should have a PhD in natural or engineering sciences, or a Diploma/Masters degree with at least extensive experience in the area of image analysis. It is essential to have a very strong background in image processing of digital images with biological and/or medical applications. Solid programming skills, excellent knowledge of image processing algorithms and software development environments and commonly used image analysis software packages are required. A sound knowledge of cutting edge advanced image acquisition methods and their optimisation to enable efficient image analysis would be an advantage. Excellent organization skills and the ability to work in an interdisciplinary and international team environment are expected. As this position has the potential to expand into a small team, experience in supervising and/or training undergraduate and graduate students is beneficial, but not essential. The successful candidate will be closely associated with the Advanced Light Microscopy Facility and the Electron Microscopy Core Facility.

More informations at: https://www.embl.de/jobs/searchjobs/index.php?ref=HD_01083&newlang=1&b=%2Fjobs%2Fsearchjobs%2Findex.php%3Fnewlang%3D1%26loc%3D0%26pos%255B%255D%3D0%26srch_trm%3D%26list%3DSearch

Post-doctoral researcher

Institut de Génomique Fonctionnelle de Lyon (IGFL), France

How do animal regenerate?

Computacional analysis of live imaging data

The team of Michalis Averof, at the Institut de Génomique Fonctionnelle de Lyon (IGFL) in France, is recruiting a post-doctoral researcher to study the morphogenesis of regenerating legs. The project will investigate the cell dynamics that underpin leg formation during regeneration (the spatiotemporal patterns of cell division, apoptosis, cell rearrangements and cell shape changes) and ask whether this process mirrors the mechanism of leg development in the embryo. The project is funded by an ERC Advanced Grant.

Candidates should have a strong background in computational analysis of live image (timelapse) recordings, preferably in the context of morphogenesis. The research will be carried out in the crustacean Parhyale hawaiensis, a new experimental model that combines good regenerative abilities with genetic tractability and live imaging (see Science 343: 788-791). At present, Parhyale is the only model organism where the entire process of limb regeneration can be imaged continuously at single-cell resolution (eLife 5: e19766, eLife 5: e21583). Transgenic lines expressing fluorescent markers and live imaging methods are well established in the lab, and quality image datasets are already available.

The researcher will be integrated in the Averof lab (www.averof-lab.org), in the new laboratories of the IGFL at the École Normale Supérieure de Lyon, an exciting environment for research at the interface of development, physiology and evolution and genomics. The working language of the team is English.

The researcher will receive a salary and health/social security coverage from the CNRS. The contract will be initially for one or two years, with possible extensions until the end of the project (December 2021). The starting date is negotiable.

This call has an open deadline; applications will be examined until the relevant position is filled. Potential applicants are encouraged to contact Michalis Averof as early as possible, sending a brief description of interests and a CV to michalis.averof@ens-lyon.fr.

POSTDOCTORAL POSITION

UNIVERSITAT POMPEU FABRA (BARCELONA, SPAIN)
DEPARTMENT OF EXPERIMENTAL AND HEALTH SCIENCES (DCEXS)DEPARTMENT OF ENGINEERING AND INFORMATION AND COMMUNICATION TECHNOLOGIES (DTIC)

We are interested in understanding how morphogenesis and cell fate acquisition are intertwined during neurogenesis upon the embryonic development of the Central Nervous System. Our aim is to build an expandable open-source platform to integrate data from labels of molecular gene expression, clonal growth, functional clusters and definitions of anatomical regions: the digital Z-hindbrain. This open-access IT resource will help us to expand our knowledge of how the brain is functionally organized, and therefore for advancing brain research, medicine, and brain-inspired information technology.

The fellow will work in collaboration between two groups: Piella’s lab at DTIC (Campus Poble Nou, https://www.upf.edu/web/simbiosys), and Pujades’ lab at DCEXS (http://pujadeslab.upf.edu) that is located within the PRBB, a vibrant research park harboring several research institutions.

CANDIDATE REQUIREMENTS:

We are seeking for highly motivated and enthusiastic candidates with background in biological/medical image analysis and, in particular, in image registration, and spatiotemporal alignment techniques such as statistical atlases. Programming experience is required.

Candidates must have good English communication skills.
The fellowship covers the salary for 1 year, with the possibility of being renewed.

The fellow will benefit from working in two dynamic groups, at university departments that recently received the Maria de Maetzu Award for their scientific excellence.
Interested candidates are encouraged to send a letter of interest, CV, and contact details of 2 referees either to Gemma Piella (gemma.piella@upf.edu) or Cristina Pujades (cristina.pujades@upf.edu).

PROCESSING AND IMAGE ANALYSIS ENGINEER IN FLUORESCENCE MICROSCOPY

INSTITUT CURIE (Paris, FRANCE)

The Genetics and Development Biology Unit (ugbdd.curie.fr) at Institut Curie is a multidisciplinary department whose main objective is the study of events controlling cell dynamics during embryonic development. The research teams intensively use optical fluorescence microscopy to visualize in real time different biological processes in various animal models (Drosophila, zebrafish and mouse). Within the Labex-DEEP program (labex-deep.fr), we are looking for a bioimage analyst.

Missions

* Designing and implementing tools for image analysis and processing using ImageJ and/or Matlab.
* Set-up advanced workflow. e.g. image segmentation, quantify intracellular protein distribution, pattern recognition, tracking of dynamic particle …
* Work with scientists for writing / implementing algorithms for solving 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.

Skills

* University degree (Master, PhD), engineering school or equivalent degree with a strong specialization in image processing and analysis.
* Experience in the development of tools to process and analyse multidimensional fluorescence microscopy datasets using ImageJ (macro scripting and writing java plugins) and/or Matlab.
* Good knowledge of segmentation algorithms, object tracking, pattern recognition.
* Ability to work in teams while managing multiple projects simultaneously with a high degree of technical autonomy.
* Able to communicate in English.

Please send your CV, cover letter and contact information for two references to: recrutement.labex.deep@curie.fr

Contract: Defined time contract (18 months renewable). Salary depending on experience and qualifications.

Applications will be reviewed when they are received.

BioImage Analyst

Postdoctoral research fellow in 3D image analysis of intra-tumor heterogeneity

Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Translational Medicine and Chemical Biology

A postdoctoral position in 3D image analysis of intra-tumor heterogeneity is immediately available in the Crosetto lab for Quantitative Biology and Technology (https://bienkocrosettolabs.org/) with the goal of studying phenotypic, genetic, and transcriptional intra-tumor heterogeneity by high-throughput microscopy imaging of serial tissue sections from different tumor types and hundreds of patients. The position is funded through a 33 million SEK research grant (Integrated Visualization of Intra-Tumor Heterogeneity) recently awarded to Dr. Crosetto by the Swedish Foundation for Strategic Research (SSF).

Research environment
The Crosetto lab is part of the Science for Life Laboratory (SciLifeLab) situated at the Karolinska Institute Solna campus. SciLifeLab is an interdisciplinary center for molecular biosciences with focus on health and environmental research, bringing under the same roof groups from four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center features state-of-the-art technology platforms, including next-generation sequencing, high-throughput histology, super-resolution microscopy, proteomics, image analysis, and bioinformatics.

The successful candidate will join an interdisciplinary and dynamic team of international researchers, including clinicians, biologists, biotechnologists, engineers, computer scientists, and physicists. Our mission is to transform the way we understand complex biological phenomena and diseases such as cancer, by integrating next-generation sequencing technologies, single-molecule microscopy methods, and advanced computational tools.

Duties
The main goals of the project are to develop image-based metrics of phenotypic, genetic, and transcriptional intra-tumor heterogeneity in various cancer types and clinical samples, and to assess whether these metrics are predictive of clinical endpoints such as response rate and overall survival.

Specific tasks of the position will include:

Develop tools for 2D and 3D automatic segmentation of DAPI-stained nuclei in z-stacked tissue section scans
Develop deep learning approaches (convolutional networks) to automatically identify different cell types (tumor cells, stroma, blood vessels, etc.) in the images analyzed, with particular emphasis on identifying different immune cell types
Apply spatial statistics methods to study the spatial distribution of different cell types, and define metrics of intra-tumor heterogeneity to be correlated with clinical endpoints (response rate, survival)
Use 3D image data to construct high-resolution maps of the intra-tumor vasculature and model tumor growth

The successful candidate will be jointly supervised by Dr. N. Crosetto (supervision on the biological and medical part of the project) as well as by Dr. K. Smith, Director of the BioImage Informatics national facility at SciLifeLab Stockholm (supervision on the image analysis part).

Entry requirements
A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc.

The successful candidate shall hold a PhD in computer science and/or physics and/or mathematics and clearly demonstrated prior experience in image processing, machine learning, and statistical analysis (not necessarily for biological applications). Proficiency in various programming languages (C++, Python, Matlab, bash) and knowledge of software engineering principles (code optimization, parallel computing) is mandatory. Familiarity with web applications design and visualization experience is a plus. Prior use of Matlab and/or Python for image analysis and familiarity with a deep learning framework (Tensorflow, Caffe, Torch) is highly desirable. Candidates with demonstrated expertise in biostatistics are particularly encouraged to apply. A strong motivation to work in an interdisciplinary and collaborative environment, and a strong sense of mission and self-drive are indispensable.

More information at https://ki.mynetworkglobal.com/en/what:job/jobID:143481/where:4/

Last application date 30.Apr.2017 11:59 PM CET

Career consultation: Bioimaging Analysts today!

NEUBIAS, the network of BioImage Analysts funded by COST until 2020, aims to promote the profession of Bioimage Analysts in the Life Science. To this end, the network will devise best-practice guidelines for the career path of these experts, design surveys to scan for existing curricula of BioImage Analysts, and will aim to define a consensus Curriculum in Advanced BioImage Analysis and to create a Job offer repository.

If you are a BioImage Analyst or identify as an important part of your job to be involved in using/developing Image Analysis within Life science, please fill up this questionnaire and help us describing the state of the art of this new profession and identifying the bottlenecks: https://eubias.org/NEUBIAS/careers/

Author: Julia Fernandez-Rodriguez, Leader Work Group 7

BioImage Analyst & Microscopist

BioImage Analyst & Microscopist graduate/postdoc position

We are recruiting a highly motivated candidate for the Confocal Microscopy Unit at the Spanish National Cancer Research Centre (CNIO) in Madrid – Spain
Place of employment: Confocal Microscopy Unit Spanish National Cancer research Centre (CNIO) Madrid, Spain, http://www.cnio.es/ing/index.asp

Job description:
•   Providing support to users of confocal microscopes during acquisition, processing and analysis of image data
•   Development of new methods and tools for image processing, analysis and High Content Analysis.
•   Performing statistical analysis support of image data using.
Qualification expected:
•   Graduate/postdoc eager to work with microscopes and to contribute to biomedical applications
•   IT skills including SW development, e.g. in MATLAB, ImageJ, JAVA or Python.
•   Knowledge of image analysis and microscopy, especially advanced optical microscopic techniques (confocal and multiphoton microscopy) appropriate training will be provided.
•   Ability to work independently and learn permanently.
•   Responsibility.
•   Flexibility and strong communication skills for effective collaboration with research teams and users.
•   Fluency in written and spoken English.
Benefits:
•   Participation in relevant short-term courses and congresses.
•   Possibility to be directly involved in scientific research.
•   Friendly and creative environment.
If you are interested in applying for this position, please send your CV and covering letter, with the reference TSMIC5, explaining your motivation and suitability for this position to: personal@cnio.es, more info: http://www.cnio.es/es/empleo/ofertas-amp.asp?codigo=1872