Microscopy career scientist position in spatial profiling and tissue imaging

Harvard Program in Therapeutic · Boston, Massachusetts
Department Harvard Program in Therapeutic
Employment Type Full-Time
Minimum Experience Experienced

Microscopy career scientist position in spatial profiling and tissue imaging

About the position

The Harvard Medical School Laboratory of Systems Pharmacology (LSP) seeks a PhD-level microscopist interested in a career scientist position within an interdisciplinary team of professionals seeking to revolutionize how cancers and other diseases are diagnosed and treated. The team focuses on the use of 2D and 3D highly-multiplexed imaging of cells, tissues, and tumors, conventional and spatial transcriptomics, and the use of software tools based on machine-learning. The position provides a unique opportunity to work with experts in human disease, cell and tissue biology, visual computing, and machine learning; details can be found at https://www.tissue-atlas.org/.  Reporting to the Director of Microscopy and Computer Vision, this position is an outstanding alternative to a postdoc (or second postdoc) for an individual who thrives on scientific challenges and seeks to work as part of an interdisciplinary academic team.


The applicant must have a PhD in a natural science or biomedical engineering and research experience in cell, tissue or developmental biology, or related disciplines that involve extensive use of optical microscopes. Ideal candidates will have experience in both microscopy instrumentation and computational data analysis and familiarity with (or a readiness to learn) best practices in image acquisition and data processing. Experience with tissue biology, histology, or pathology in mouse models or human disease is a plus. Extensive formal and informal opportunities for career development as a research scientist or engineer are possible.


Successful candidates will join a team of a dozen PhD and MSc-level career scientists working to advance the state of the art in spatial profiling of tissues.  The tissue imaging team at the LSP collaborates with over a dozen research groups from across the US and Europe and the candidate will have an opportunity to travel to and publish with these labs and also attend scientific meetings.  The candidate will become proficient in high-plex tissue imaging, digital pathology, and machine-learning tools for image analysis and have exposure to spatial transcriptomics methods and imaging mass spectrometry. The team operates a number of high performance confocal, 3D sectioning, and high content scanning instruments.


This position is available with a flexwork option for applicants living in or planning to relocate to a location commuting distance to campus (Massachusetts, Rhode Island, New Hampshire). At least three days per week of on-site work at the HMS campus in Boston MA is required however.

About the Laboratory of Systems Pharmacology

The Laboratory of Systems Pharmacology (LSP) is a highly collaborative, multidisciplinary research and education program located in the center of Harvard Medical School (HMS). The LSP engages in a wide variety of research projects focused on cancer, Alzheimer’s disease, chronic pain, and infectious disease. Career bench scientists, software and instrumentation engineers, and data analysts play essential roles in these projects. The LSP has a very active software team that oversees the development and implementation of open-source tools for data integration and analysis, image management, machine learning, and visualization.


The LSP is a component of the Harvard Program in Therapeutic Science (HiTS - http://hits.harvard.edu), which aims to reinvent the fundamental science underlying the development of new medicines and their use in individual patients.  LSP staff, faculty, administrators, and students represent a wide range of ages, races, interests, and backgrounds come together in pursuit of common goal of fundamentally improving human health. Harvard is an Affirmative Action/Equal Opportunity Employer and applications from women and persons of color are strongly encouraged.


Former LSP members are now faculty members in US, Europe, and Asian universities, lead core facilities or interdisciplinary projects at leading academic research institutions, have started software and biotech companies using the lab’s technologies, or have assumed leadership positions in the pharmaceutical industry.


  • Work closely with wet-bench scientists, data analysts and software engineers from the LSP, affiliated research hospitals, and other universities to design imaging experiments, advise on controls, and train individuals on best practices on instrument usage
  • Perform original research in collaboration with LSP trainees, staff and faculty and contribute to peer-reviewed manuscripts
  • Provide hands-on support with deploying image processing tools to users having a diverse set of backgrounds
  • Stay up-to-date on the latest developments in the field by reading relevant scientific literature, attending seminars, and scientific meetings
  • Learn to deploy tools and pipelines developed in LSP (https://mcmicro.org/) and uphold imaging metadata standards (https://github.com/miti-consortium/MITI) across a diverse range of computing environments for terabyte-scale imaging data
  • Other duties will include documenting projects, overseeing the maintenance of microscopes, data management, and participation in LSP lab meetings and other project meetings.


Application Process

Please submit a cover letter, a current CV and two or more references via the Bamboo HR portal (https://hitsedu.bamboohr.com/). Incomplete applications will not be reviewed. The cover letter must highlight your past contributions to projects that have featured optical microscopy as a central theme. Examples where you have provided technical consultation and experimental design to other scientists are highly encouraged. If you have developed open-source image analytical methods, you may include links to GitHub/GitLab as appropriate. Promising candidates will be contacted for a Zoom interview and (possibly remote) in-person meetings with lab members. The LSP currently operates a hybrid work model with scientific staff on-site 3-5 days per week depending on job function (subject to change based on Harvard, Federal and State pandemic policy).

Mandatory qualifications

  • PhD (or the European equivalent) in a natural science, biophysics, optical engineering or biomedical engineering and research experience in cell, tissue or developmental biology in or related disciplines that involve extensive use of optical microscopy
  • Familiarity with one or more multidimensional fluorescence microscopy methods such as high-content screening of cell lines, live-cell imaging, digital pathology, 3D optical sectioning with confocal or lightsheet microscopy or related methods
  • Experience with basic maintenance of microscopes (i.e., cleaning objective lenses, clearing old data)
  • Experience with basic image processing tasks such as image segmentation, registration, spot detection; experience with 3D visualization software (commercial or open source) is a plus.
  • Experience with sample preparation, experimental design and use of microscopes to obtain quantitative date on biological specimens
  • Excellent oral and written communication skills

Desired qualifications

  • Proficiency with Python scientific packages (scikit-image, openCV) and/or MATLAB image analysis toolbox including performance tuning and debugging and versioning tools
  • Experience with deep learning packages for image processing, e.g., tensorflow, PyTorch
  • Experience with one or more of the following: Zeiss ZEN, GE INCell Analyzer, Molecular Devices MetaXpress, OME/OMERO, and/or GE SoftWorX
  • Experience in handling large-scale datasets


Compensation and Benefits

  • Salaries are based on level of experience and competitive with similar positions at other research institutions. As a guide, for newly graduated students salaries are 40-50% higher than standard NIH postdoctoral salaries
  • Signing bonus to assist with moving to the Boston area and securing housing.
  • Exceptional set of Harvard-provided health and welfare benefits (https://hr.harvard.edu/health-welfare-benefits)
  • New desktop and/or laptop computer and productivity and developer tools (e.g., a MATLAB and Adobe Creative Cloud license, Dropbox Business account)
  • Desk and office space in the LSP as needed in newly renovated space in the historic Armenise or Warren Alpert Buildings on the HMS Quadrangle
  • Opportunity to attend two conferences or scientific meetings per year in the US or Europe
  • Extensive opportunities to interact and network with programmers and cancer biologists developing next-generation approaches to health care


Thank You

Your application was submitted successfully.

  • Location
    Boston, Massachusetts
  • Department
    Harvard Program in Therapeutic
  • Employment Type
  • Minimum Experience