Senior Biomedical Imaging Engineer

(ID: 2025-1385)

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with premier research organizations and facilities including multiple institutes at the National Institutes of Health (NIH) and other public and private organizations. 

 

Benefits We Offer:

• 100% Medical, Dental & Vision Coverage for Employees
• Educational Benefits for Career Growth
• Paid Time Off (Including Holidays)
• Employee Referral Bonus
• 401K Matching
• Flexible Spending Accounts:
  • Healthcare (FSA)
  • Parking Reimbursement Account (PRK)
  • Dependent Care Assistant Program (DCAP)
  • Transportation Reimbursement Account (TRN)

 

Overview:

At the intersection of high-throughput drug discovery and cloud-native engineering, we are building the foundational infrastructure for a "lab-in-an-automated-loop". We produce petabyte-scale imaging data across global research sites and are now moving to modernize how that data is processed, analyzed, and stored.

We are not looking for a generalist. We need a specialist who understands that an imaging pipeline is only as good as the scientific data it produces. You will be the technical lead responsible for migrating complex imaging logic into a modular, stateless Nextflow ecosystem that supports consistent scientific decision-making at a global scale.

 

The Opportunity: Your Impact

We are seeking a Senior Biomedical Imaging Engineer with deep biomedical Imaging expertise. You will be responsible for refactoring high-priority imaging assays and moving them from interactive, platform-dependent workflows into headless, portable, and highly optimized Nextflow processes.

You must be an imaging expert first. You need to understand what is happening to the pixels, how feature tables are derived, and why a specific segmentation mask or QC metric is critical for the downstream science.

 

What You’ll Do:

• Nextflow Refactoring & Architecture: Identify imaging pipeline components suitable for direct implementation in Nextflow and refactor them into modular, reproducible processes that mirror or improve upon validated behavior.
• Deep Imaging Data Analysis: Define and document required inputs, intermediate outputs (segmentation masks, feature tables), and final plate-level summaries, ensuring the engineering supports the scientific intent.
• Architect for Heterogeneous Hardware: Design Nextflow configuration profiles that allow identical workflow definitions to run across diverse environments, from high-end GPU clusters (Nvidia L40s) with SLURM to legacy on-premise HPC nodes.
• Headless Integration: Lead the development of scripts and wrappers that enable headless execution of imaging logic, integrated directly into a GCP Workflows-based automated control system.
• Scientific Validation: Design and execute regression checks to ensure that refactored Nextflow pipelines produce outputs equivalent to legacy systems within strict scientific tolerances.
• Modular Pipeline Design: Ensure every step in the pipeline is as stateless and modular as possible to allow for rapid refactoring and reuse across different imaging assays.
• Integrate the “Lab Loop”: Collaborate with engineers to manage data handoffs between on-premise edge infrastructure and cloud-based system-of-record databases (PostgreSQL/ARC).

 

What You’ll Bring (Required Qualifications):

• A passion for the craft of engineering: you believe that scientific pipelines should be modular, stateless, and elegant.
• Advanced Nextflow Mastery: Proven experience architecting and deploying complex,