About the ELMI

ELMI was created in 2001 to establish a unique communication network between European scientists working in the field of light microscopy and the manufacturers of their equipment.

Advanced Image Analyst Specializing in Deep Learning, Rockefeller University NYC, USA

, by sterjung in Jobs

Job description

The candidate will contribute to the development of a new, integrated platform for the acquisition, processing, and analysis of data from pre-commercial light-sheet instruments for microscopy on living cells.

Funded initially by a five-year Beckman Foundation grant to the Rockefeller University, they will work in close collaboration with microscope engineers, biologists, physicists, bioinformaticians, and computer scientists in an international and interdisciplinary environment.  The candidate will implement and design deep-learning-based computational workflows to extract meaningful information from light-sheet data obtained from various experimental organisms (cultured cells, nematode worms, zebrafish, mammalian embryos) and biological models.

As a staff member in the Bio-Imaging Resource Center (BIRC) and working together with the Bioinformatics Resource Center (BRC), the candidate will liaise between the existing microscopy and image analysis and informatics staff and the research scientists.  The position will involve providing training and assistance to researchers through approaches including workshops, seminars, laboratory meetings, and regularly scheduled help-desk sessions.  Using both open-source packages and commercial image analysis software, the candidate will also advise other staff members in selecting the most suitable workflows to quantitatively analyze image data acquired with a variety of imaging modalities. In addition, the candidate will be expected to collaborate with all research scientists using the light-sheet microscopes and facilitate the use of deep-learning methods by the whole Rockefeller research community.  The candidate will also assist in piloting the implementation of the OMERO database to store, manage, and process images acquired on the new light-sheet systems, to propagate the use of OMERO throughout the BIRC and eventually the entire Institution.

The candidate should have:

  •   A Ph.D. or equivalent in biology, bioinformatics, computer science, or a related field;
  • Experience in developing bioimage analysis tools and in working with biological or medical images;
  • Knowledge and ability in open-source image analysis and deep-learning frameworks, for example, DeepImageJ, Ilastik, Napari, ImJoy, CellProfiler, ZeroCostDL4Mic, and KNIME;
  • Experience with commercial image-analysis software such as Imaris, Arivis, and Huygens (preferred);
  • Broad knowledge of the use of high-level programming and scripting languages (Java/Python/R/MATLAB) in the analysis of biological imaging data;
  • Proficiency in version control (Git) and the dynamic documentation of software code (jupiter/rmarkdown).

The candidate must be enthusiastic, rigorous, and motivated; have excellent interpersonal and communication skills, and possess the flexibility required to work in a service-oriented environment. In addition, they should be a self-starter with a proven ability to initiate collaborative projects and introduce colleagues from different backgrounds to advanced image-analysis methods.

Follow your passion for excellence in science and join our researchers in the pursuit of science for the benefit of humanity.

How to apply

We offer a competitive salary, comprehensive benefits, and a collaborative working environment.

Please visit the URL below and apply to the job code “IRC26285”.  Please make sure to upload your resume and a cover letter:


The Rockefeller University is an Equal Opportunity Employer – Minorities/Women/Disabled/Veterans