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Rockefeller University

Job Description

We provide members of the University and their visitors with a wide spectrum of microscopy equipment and image analysis software packages, together with extensive training in their use. Systems include state-of-the-art optical imaging using widefield, confocal, multiphoton, light-sheet and super-resolution microscopy. We also provide consultation on sample preparation and immunolabeling procedures. We train researchers to use the microscopes and image acquisition software themselves, providing assistance when necessary to ensure collection of high quality images. Staff also conduct more complex work on a collaborative basis with the scientists.

The center currently houses several widefield fluorescence/transmitted light microscopes (Zeiss and Olympus), two DeltaVision Image Restoration microscopes (API/GE Healthcare), three laser scanning confocal microscopes (a Zeiss LSM 780, a Leica SP8 and a Zeiss LSM 880 NLO system), a Yokagawa spinning disk confocal microscope (Zeiss/Spectral Applied), an FV1000MPE Twin upright multiphoton system (Olympus), a multi-line STORM/TIRF system (Nikon) fitted with widefield-FLIM and TIRF-FLIM capabilities (Lambert Instruments), an LCV110 "VivaView" Incubator Microscope (Olympus), a Yokawawa CV1000 "CellVoyager" environmental spinning disk system (Olympus), an Ultramicroscope light sheet system (LaVision BioTec), a laser microdissection system (MMI), and an OMX 3D-SIM super-resolution microscope (API/GE Healthcare). Most of the systems are fitted with environmental chambers for live cell imaging.

The center has five full-time research support staff including the director. The center is staffed during business hours and under an open-access model, trained investigators can use the facility 24/7. In addition, many of the systems can be operated remotely via the center's on-line facility management software.

Detailed Description
Funded initially by a five-year Beckman Foundation grant to the Rockefeller University, the Image Analyst 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. The Image Analyst will implement and design deep learning-based computational workflows in order to extract meaningful information from light-sheet data obtained from a variety of different 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 Image Analyst will liaise between the existing microscopy and image analysis and informatics staff and the research scientists. Responsibilities include working in close collaboration with microscope engineers, biologists, physicists, bioinformaticians, and computer scientists in an international and interdisciplinary environment, and will involve the provision of 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 Image Analyst will also advise other staff members in selecting the most suitable workflows to quantitatively analyze image data acquired with a variety of imaging modalities. The Image Analyst will be expected to collaborate with all research scientists using the light-sheet microscopes and to facilitate the use of deep-learning methods by the whole Rockefeller research community. Additional responsibilities include assisting 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.

Job Requirements
Ph.D. or equivalent in biology, bioinformatics, computer science, or a related field required. Experience in developing bioimage analysis tools and in working with biological or medical images required. Knowledge and ability in open-source image analysis and deep-learning frameworks, such as DeepImageJ, Ilastik, Napari, ImJoy, CellProfiler, ZeroCostDL4Mic, and KNIME, a must. 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 required. Must have proficiency in the use of version control (Git) and the dynamic documentation of software code (jupiter/rmarkdown). Must be enthusiastic, rigorous, and motivated, have excellent interpersonal and communication skills, and possess the flexibility required to work in a service-oriented environment. Must be a self-starter with a proven ability to initiate collaborative projects and to introduce colleagues from different backgrounds to advanced image-analysis methods.


New York, NY