Senior Biomedical Imaging Engineer

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.

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.

• 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).

• 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, production-grade pipelines in Nextflow for a research or clinical environment.
• Imaging Domain Expertise: Professional or academic background in Bioimage Informatics or Imaging Science. You must deeply understand image analysis algorithms, HCS data structures, and spatial metadata.
• Scientific Mindset: You have experience defining QC metrics and interpreting scientific outputs for high-throughput imaging.
• Infrastructure Fluency: Deep experience with Linux/Unix, HPC schedulers (SLURM), and optimized execution on Nvidia GPU architectures.
• Cloud Literacy: Experience working within Google Cloud Platform (GCP) or similar cloud environments for data orchestration and storage.
• Containerization Expert: Proficient in using Docker or Singularity to ensure that every step of the imaging process is hermetic and reproducible.

• SImA/Signals Familiarity: Experience with Revvity Signals Image Artist (SImA) is a strong plus, though our team already includes dedicated SImA specialists to support your refactoring efforts.
• GCP & Cloud Orchestration: Experience with Google Cloud Platform and GCP Workflows for orchestrating “lab-in-the-loop” automation.
• Programming Depth: Strong proficiency in Python or C++ for developing custom imaging transformation steps.
• Pharma R&D Experience: Experience working with high-throughput assay data and system-of-record databases like PostgreSQL.

The diversity of Axle’s employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment-based age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.

Accessibility: If you need an accommodation as part of the employment process, please contact [email protected]

Disclaimer: The above is meant to illustrate the general nature of work and level of effort being performed by individual’s assigned to this position or job. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job or responsibilities as needed.

This role has a market-competitive salary with an anticipated base compensation range listed below. Actual salaries will vary depending on a candidate’s experience, qualifications, skills, and location.