Computational Pathology Scientist (Halo/Visiopharm/QuPath/High-Plex image Analysis)

Title: Scientist III, Computational Pathology Can be Hybrid or remote in South San Francisco, CA

Purpose:

• The Precision Medicine Pathology team drives the scientific strategy for translational tissue-based biomarker development & discovery target validation/MOA projects, leads pathology collaborative programs, conducts histopathological evaluation & analysis of IHC & spatial biology technologies, and provides technical/scientific leadership to histotechnicians & pathology scientists.
• The successful candidate will have advanced knowledge and experience analyzing spatial transcriptomics and proteomics data generated on the CosMx SMI and PhenoCycler Fusion platforms.

Responsibilities:

• Implementation of different scripts and pipelines for spatial transcriptomics data analysis and analysis of high-plex PhenoCycler Fusion (CODEX) images.
• Independently performing end-to-end high-plex image analysis (tissue classification, cell segmentation, detection of marker positivity, cell phenotyping, unsupervised clustering, neighborhood analysis, proximity analysis).
• Acting as a subject matter resource and training other team members in spatial analysis tasks.
• Collaborating with pathologists and digital pathology scientists to support spatial biology projects.
• Presenting the results and findings from spatial biology studies to stakeholders.

Qualifications:

• MSc, PhD, or equivalent degree in biological sciences / computational biology / engineering / computer science / informatics
• Fluency in Python and R
• Experience in implementing and utilizing open-source scripts and pipelines for high-plex image analysis
• Experience in quantitative digital pathology analysis platforms such as Halo, Visiopharm, QuPath
• Close familiarity with tissue microscopic anatomy and histology (normal and diseased) is a plus
• Excellent verbal communication skills are required including the demonstrated ability to effectively and clearly summarize results for presentation and report generation
• Strong motivation, attention to detail, ability to think independently and fully integrate into a high achieving team environment
• Ability to multi-task and manage multiple projects

Job Type: Contract

Pay: $76.00 - $78.00 per hour

Expected hours: 40 per week

Benefits:

• Health insurance

Education:

• Doctorate (Preferred)

Experience:

• high-plex image analysis: 5 years (Preferred)
• Halo, Visiopharm, QuPath: 5 years (Preferred)
• analyzing spatial transcriptomics and proteomics data: 5 years (Preferred)
• quantitative digital pathology analysis: 5 years (Preferred)

Work Location: Remote