Computational Scientist I - Digital Pathology Image Analysis

Broad Institute; Cambridge (MA); On-site; USD 110,000 - 150,000; Full time

Benefits offered by this job

Medical insurance

401(k) plan

Paid holidays and time off

Job summary

The Broad Institute of MIT and Harvard is seeking a highly motivated Computational Scientist I to join the Surfaceome Target Discovery team. You will develop and deploy quantitative image analysis workflows for whole-slide tissue images, focusing on IHC and mIF panels to drive surface target validation in tumor tissues.

Responsibilities include designing ML-based digital pathology methods, building scalable pipelines, and collaborating with pathologists and translational researchers to produce

Qualifications

• Master's or Ph.D. in Biomedical Engineering, Bioinformatics, CS, or related field with quantitative life sciences focus.
• 4+ years of relevant experience for Master's degree holders.
• Hands-on experience with QuPath and image analysis workflows.
• Proficiency in Python, R, and Groovy for analysis and automation.

Responsibilities

• Design, develop, and optimize ML-based digital pathology methods for segmentation, classification, and spatial analysis.
• Build scalable preprocessing, QC, and analysis pipelines for TMA and whole-slide imaging datasets.
• Validate imaging workflows and classifiers with benchmarking and external datasets.
• Collaborate with pathologists and scientists to assess quality, artifacts, and tissue integrity.
• Translate biological questions into quantitative imaging metrics and outputs.
• Coordinate analyses across cross-functional teams and maintain reproducible workflows.

Skills

Machine learning

Image analysis

Groovy scripting

Python

R

Team collaboration

Education

Master's or Ph.D. in Biomedical Engineering

Tools

QuPath

Akoya PhenoImager/Opal

VISIOPHARM

Docker

AWS/GCP

TensorFlow/PyTorch

Job description

Description & Requirements

The Broad Institute of MIT and Harvard is the world's leading biomedical research institute dedicated to the bold mission of using the full power of genomics to transform the understanding and treatment of disease. We seek to describe all of the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

We are seeking a highly motivated and skilled Computational Scientist I to join our Surfaceome Target Discovery team and the Getz lab. In this role, you will play a critical part in accelerating our target validation pipeline by developing, optimizing, and deploying quantitative image analysis workflows. You will work closely with the Broad Cancer Cell Line Factory, the Dana-Farber Cancer Institute (DFCI) Pathology Core, and the Sellers lab in a highly collaborative and multidisciplinary research environment.

The ideal candidate will have extensive hands-on experience handling whole-slide tissue images, specifically single plex/multiplex Immunohistochemistry (IHC) and multiplex Immunofluorescence (mIF) panels. You will translate target expression patterns, immune microenvironment, and spatial biology into robust, reproducible quantitative metrics to drive surface target validation in patient tumor and normal adult tissue microarrays.

Key Responsibilities

• Design, develop, and optimize machine learning and AI-based methods for digital pathology applications, including image segmentation, classification, spatial analysis, and predictive modeling using QuPath and other imaging platforms.


• Build and maintain scalable pipelines for preprocessing, quality control, and analysis of tissue microarray (TMA) and whole-slide imaging datasets generated from high-plex multiplex immunofluorescence (mIF) and chromogenic IHC assays.


• Develop and execute validation strategies for imaging workflows and classifiers through benchmarking, performance assessment, and external dataset validation to ensure analytical robustness and reproducibility.


• Collaborate with pathologists and scientists to perform image quality assessment, evaluate classifier accuracy, and identify imaging artifacts, staining variability, segmentation errors, and tissue integrity issues prior to downstream analysis.


• Partner with pathologists, assay biologists, translational researchers, and/or data scientists to translate biological and clinical questions into quantitative imaging metrics and actionable analytical outputs.


• Coordinate imaging analyses and deliverables across cross-functional teams to support project goals, timelines, and study milestones.


• Maintain well-documented, reproducible workflows, including SOP-compliant analysis records, QC documentation, version-controlled code repositories, and organized large-scale imaging datasets.

Qualified Candidates Should Have:

• Master's or Ph.D. degree in Biomedical Engineering, Bioinformatics, Computer Science, Computational Biology, or a related quantitative life sciences discipline with expertise in digital pathology and image analysis.
  
  
  • Candidates with a Master's degree should have at least 4+ years of relevant industry or academic research experience.
  
  
  
  


• Demonstrated hands-on experience with QuPath, including cell detection, tissue microenvironment analysis, classifier development, and custom Groovy scripting for workflow automation and scalable image analysis.


• Strong understanding of tissue-based imaging assays and spatial biology technologies, including H&E, chromogenic IHC, mIF, and related imaging platforms such as Akoya PhenoImager/Opal, COMET, or equivalent systems.


• Proficiency in Python, R, and/or Groovy for image analysis, spatial data analysis, statistical modeling, and workflow development; experience with deep learning frameworks (e.g., PyTorch or TensorFlow) for tissue segmentation and classification is highly desirable.


• Experience developing reproducible and well-documented computational workflows, including version-controlled code management and structured data organization practices.


• Strong analytical, problem-solving, and communication skills, with the ability to work effectively in multidisciplinary research environments.

Preferred Qualifications:

• Experience with commercial digital pathology platforms such as Indica Labs HALO/HALO AI, Visiopharm, or related image analysis software.


• Familiarity with cloud-based computing environments (AWS, Google Cloud Platform) and containerized workflow development using Docker or similar technologies.


• Experience supporting translational oncology, immuno-oncology, or biomarker discovery programs in academic, biotech, or pharmaceutical research settings.


• Demonstrated scientific contributions through publications, collaborative projects, or presentations involving computational pathology, spatial biology, or quantitative imaging analyses.

The expected base pay range for this position as listed above is based on a 40 hour per week schedule. Broad provides pay ranges representing its reasonable and good faith estimate of what the organization reasonably expects to pay for a position at the time of posting. Actual compensation will vary based on factors including but not limited to, relevant skills, experience, education, qualifications, and other factors permissible by law.

At Broad, your base pay is just one part of a comprehensive total rewards package. From day one, this role offers a competitive benefits package including medical, dental, vision, life, and disability insurance; a 401(k) retirement plan; flexible spending and health savings accounts; at least 13 paid holidays; winter closure; paid time off; parental and family care leave; and an employee assistance program, among other Broad benefits.

The Broad Institute is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, national origin, religion, age, color, sex, disability, protected veteran status, or any other characteristic protected by local, state, or federal laws, rules, or regulations.

Should you need a reasonable accommodation to complete the application or interview process, please contact [e-mail] for assistance.