Senior Computational Imaging Scientist – AI & Cloud Pathology

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 129,000 - 211,000; Full time

Benefits offered by this job

401(k) plan

Pension

Vacation benefits

Medical, dental, vision benefits

Flexible benefits

Life insurance

Job summary

Lilly is seeking a hands-on scientific leader to design, validate, and deploy enterprise-scale, cloud-based computational imaging solutions across multiple therapeutic areas. The role emphasizes reproducibility, AI-assisted coding, and responsible AI in preclinical through early clinical research.

Deep wet-lab grounding in brightfield IHC and IF workflows complements image analysis, with an emphasis on scalable pipelines, data governance, and collaboration with bench scientists and CROs.

Qualifications

• PhD (completed or imminent) in Computational Biology, Bioinformatics, Computer Science, Biomedical Engineering, Quantitative Biology, Data Science, or a related quantitative field
• Strong Python and R, with software engineering practices: Git, code review, testing, reproducibility, documentation, and containerization (Docker preferred).
• Demonstrated use of AI coding assistants and/or agentic AI systems, including critical review, validation, debugging, and quality control of AI-generated code.
• Hands-on quantitative analysis of brightfield and fluorescence microscopy, including segmentation and biomarker quantification.

Responsibilities

• Design, validate, and deploy quantitative image-analysis workflows for brightfield and fluorescence imaging: segmentation, object detection, feature extraction, biomarker quantification, colocalization, and cell/tissue phenotyping.
• Generate and evaluate samples, applying understanding of image quality to ensure biologically meaningful analysis, solving workflows end to end with bench collaboration.
• Build reproducible, scalable, cloud-based pipelines with rigorous image QC, statistical analysis, and traceability.
• Apply computer vision, machine learning, and deep learning to practical scientific problems; use AI coding assistants with rigorous validation of AI-generated code.
• Drive computational imaging strategy and translate questions into scalable analytical solutions across therapeutic areas.

Skills

Python

R

Git

Docker

Containerization

AI coding assistants

Cloud computing

Nextflow

Snakemake

SQL

Education

PhD in Computational Biology, Bioinformatics, CS, or related quantitative field

Tools

HALO

Visiopharm

Arivis Pro

AtoMx

QuPath

CosMx

Xenium

MERSCOPE

GeoMx DSP

AWS

Job description

Lilly is seeking a hands-on scientific leader to design, validate, and deploy enterprise-scale, cloud-based computational imaging solutions across multiple therapeutic areas. The role emphasizes reproducibility, AI-assisted coding, and responsible AI in preclinical through early clinical research.

Deep wet-lab grounding in brightfield IHC and IF workflows complements image analysis, with an emphasis on scalable pipelines, data governance, and collaboration with bench scientists and CROs.