Image Analysis Specialist - Waitt Advanced Biophotonics Center, Dr. Uri Manor

  • Salk Institute for Biological Studies
  • La Jolla, CA, USA
  • Apr 20, 2021
Full time Biology/Biotechnology/Life Sciences

Job Description


Application Instructions:

Employment History Include your last ten (10) years of employment history, or length of your employment history if less, including all positions (even those that are not relevant to this position) and periods of unemployment. Incomplete information could disqualify you from further consideration.


The Image Analysis Specialist will have a principal responsibility to develop machine learning-based software for image restoration and analysis. The position will collaborate with other light and electron microscopy researchers in the Biophotonics Core and the Institute to provide specific expertise for developing custom computer algorithms for complex and novel analyses of raw imaging data, computer data management and developing algorithms for microscopy operations. The position will apply existing image processing software to 2D and 3D images and videos and will also integrate data across different platforms (e.g. correlative EM). The incumbent will become familiar with the microscopes used in the facility and develop expertise in using the equipment to acquire imaging data optimized for image analysis. Consults with lab and core staff on how to properly acquire high quality quantitative microscopy image data. This is a multi-faceted job that involves the following components: machine learning, image processing and data analysis, research design and participation, and data collection and presentation.


(80%) Image Processing Algorithm Research and Development

  • Develop new image analysis algorithms using a variety of scientific programming languages.
  • Provide expertise in reconstructed 3D datasets for scientific projects, e.g. tomographic reconstructions, tracing of image objects, building 3D models from both light and electron microscopy datasets.
  • Perform and/or advise on quantitative analysis of light microscopy datasets.
  • Perform and/or advise on commercial image analysis software platforms (Metamorph and Imaris).
  • Ensure compliance with appropriate data analysis methods and research ethics.
  • Responsible for providing collaborative assistance with image analysis, e.g. image averaging, filtering, alignment, quantitative analysis, and reconstruction of 3D datasets.

(10%) Data Collection and Presentation

  • Prepare data for publication, grant applications, posters and other presentations using digital facilities.
  • Present data at department or Institute meetings.
  • Prepare images/movies for presentations.
  • Assist in preparation of manuscripts, grants, progress reports and annual protocols.
  • Prepare publication quality micrographs and plates.
  • Maintain lab notebook, including experimental design, time, methods, materials and results.

(10%) Research Design and Participation

  • Design, and carry out experiments involving collection and processing of tissues and tissue culture cells and their analysis by immunofluorescence, live-cell imaging, two-photon microscopy, TIRF microscopy, super-resolution microscopy (both PALM and SIM), automated slide scanning (both bright-field and fluorescence), laser capture microdissection and transmission and scanning electron microscopy
  • Provide innovative contributions to the design and construction of experiments for multiple research projects to obtain high quality imaging data.
  • Participate in the collection and analysis of images and application of protocols for quantification of data.
  • Keep informed of new developments and technical advances in light microscopy in the fields of molecular and cell biology by reading primary literature and microscopy and manufacturer websites.



  • Minimum 4 years of experience in computer science, physics, engineering, chemistry or biological sciences.
  • Scientific programming skills demonstrated experience in image analysis.


  • Microscopy experience
  • Tissue preparation and histology experience



  • BS degree in computer science, physics, engineering, chemistry or biological sciences, or equivalent


  • MS or PhD degree in computer science, physics, engineering, chemistry or biological sciences



  • Theoretical and practical knowledge of machine learning principles.
  • Demonstrated skill and experience in the high resolution operation of light and electron microscopes including fluorescence microscopy, confocal microscopy (both fixed and live cell), two-photon microscopy, TIRF microscopy, super-resolution microscopy (both PALM and SIM), automated slide scanning (both bright-field and fluorescence), laser capture microdissection and transmission and scanning electron microscopy.
  • Theoretical and practical knowledge of biology or related scientific field and of tissue structure on an anatomical, cellular, and molecular level.
  • Understanding both the theory and practice of various immuochemical localization labeling techniques for light and electron microscopy
  • Experience in performing experimental protocols unsupervised and in recommending modifications to procedures and protocols to meet the needs of research projects. Demonstrated ability to contribute to experimental design and assist with the analysis and interpretation of results.
  • Proven organizational and time management skills to successfully set priorities, meet established deadlines and recognize new problems with constantly changing priorities and frequent interruptions.
  • Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment. Ability to read, comprehend, and discuss research materials. Proven ability to write, edit and proofread research results. Skill at explaining difficult concepts and training users and students.
  • Ability to diplomatically and professionally with all levels of Institute staff and external contacts.
  • Proven ability to perform minor maintenance on light microscopes.
  • Comprehensive knowledge of photographic techniques including visual arts production, copy work, photographic printing and enlarging, and slide making.
  • Knowledge of standard laboratory and safety procedures.
  • Demonstrated knowledge and experience with both PC and MAC operating systems, standard business office equipment and commonly used software and tools, such as Microsoft Office, electronic mail, and the internet
  • High proficiency in a scientific programming language such as MATLAB


  • Must be willing to work in an animal-related research environment.
  • Satisfactory completion of the Institute's background investigation.
  • Willing to sign a confidentiality agreement
  • Able to work a flexible schedule based on research needs and deadlines.


This position requires constant adjusting focus, grasping, hearing, keying, seeing, sitting, talking, analyzing, calculating, communicating, reading, reasoning, writing, and working inside. 


Application Details

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