Advisor / Sr. Advisor – Computational Imaging Specialist

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

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work— but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

Position Purpose

This hands‑on scientific role sits at the intersection of computational biology, quantitative image analysis, AI‑assisted scientific computing, enterprise data science, and drug discovery, within an enterprise capability serving Lilly’s therapeutic areas (diabetes, obesity, cardiometabolic, cardiorenal, women’s health, neuroscience, immunology, and others). Operating independently as a scientific and technical domain expert, you will design, validate, and deploy enterprise‑scale, cloud‑based computational imaging solutions, emphasizing reproducibility over desktop workflows and the responsible use of AI, including AI coding assistants and agentic systems, that turn microscopy, histology, digital pathology, and spatial tissue analysis (Cellular neighborhoods, tissue organization, microenvironment features) data into decision‑driving evidence from preclinical through translational and early clinical research. Computational expertise in this role is complemented, not replaced, by hands‑on wet‑lab capability in brightfield IHC and IF workflows, grounding image analysis in practical understanding of staining, assay development, and the underlying biology. This is not a traditional bioinformatics, pathology, or standalone image‑analysis position, and it does not involve radiology or medical imaging (CT, MRI, PET).

Key Responsibilities

• Design, validate, and deploy quantitative image‑analysis workflows for brightfield (histology, H&E, chromogenic, IHC) and fluorescence (IF, multiplex IF) imaging: segmentation, object detection, feature extraction, biomarker quantification, colocalization, and cell/tissue phenotyping.
• Generate and evaluate IHC/IF samples at the bench as needed (tissue processing, staining, assay development, QC), applying this understanding of what drives image quality to ensure biologically meaningful analysis, solve workflows end to end, and collaborate effectively with bench scientists.
• Build reproducible, scalable, cloud‑based pipelines (AWS today; cloud‑agnostic by design) with rigorous image QC, statistical analysis, and traceability.
• Apply computer vision, machine learning, and deep learning, including foundation, multimodal, and generative models, to practical scientific problems; use AI coding assistants while rigorously validating AI‑generated code and outputs.
• Drive computational imaging strategy: translate scientific questions into scalable analytical solutions and deliver them to project achievements across therapeutic areas.
• Evaluate commercial and open‑source technologies, inform build‑versus‑buy decisions, and integrate vendor platforms (e.g., HALO, Visiopharm, Arivis Pro, AtoMx) and open‑source tools (e.g., QuPath) with internal Lilly capabilities.
• Contribute to enterprise imaging data architecture: repositories, metadata, governance, and lineage.
• Manage external collaborations and outsourcing with CROs, academic groups, and technology partners, including quality oversight of external data and analyses.
• Contribute to biomarker discovery and validation, publications, and presentations; champion scientific software and responsible‑AI protocols and mentor colleagues informally.

Basic Qualifications

• PhD (completed or imminent) in Computational Biology, Bioinformatics, Computer Science, Biomedical Engineering, Quantitative Biology, Data Science, or a related quantitative field

Additional Preferences

• Demonstrated experience independently designing, developing, validating, and deploying computational image‑analysis workflows.
• 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 (e.g., H&E, IHC) and fluorescence (e.g., IF, multiplex IF) microscopy, including segmentation and biomarker quantification.
• Hands‑on wet‑lab experience in brightfield IHC and IF workflows, tissue processing, staining, assay development, and QC, with the ability to independently generate and evaluate samples; complementary to, not a replacement for, the core image‑analysis expertise above.
• Experience with one or more enterprise‑grade image‑analysis platforms (e.g., HALO, Visiopharm, Arivis Pro, AtoMx, QuPath, or comparable).
• Experience developing analytical workflows in cloud environments (e.g., AWS or equivalent).
• SQL, Bash/Linux, JavaScript, and cloud‑native analytics frameworks.
• Whole‑slide imaging, confocal microscopy, and spatial tissue imaging; spatial omics platforms (e.g., CosMx, Xenium, MERSCOPE, GeoMx DSP).
• Enterprise‑scale imaging datasets and repositories, data governance, metadata, and lineage; imaging data standards (e.g., OME‑TIFF, DICOM‑WSI).
• Multimodal integration of imaging with transcriptomics, proteomics, spatial tissue analysis, and other omics datasets.
• Statistics and experimental design for imaging endpoints (power, batch effects, multiple testing); annotation and ground‑truth strategy with pathologists.
• Workflow orchestration (e.g., Nextflow, Snakemake, Airflow), ML model lifecycle management, and GPU/HPC computing.
• Vendor evaluation and management; technical, project, or people leadership experience.
• Peer‑reviewed publications and strong communication of computational results to non‑computational audiences.

Lillyis dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lillyis proudto be anEEOEmployer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status. Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx atLilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.

The anticipated wage for this position is $129,000 - $211,200 Full‑time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

Benefits

• eligibility to participate in a company‑sponsored 401(k)
• pension
• vacation benefits
• eligibility for medical, dental, vision and prescription drug benefits
• flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts)
• life insurance and death benefits
• certain time off and leave of absence benefits
• well‑being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

Company Culture

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly