Axle · 10 minutes ago
Senior Biomedical Imaging Engineer
United States
Full-time
Remote
Senior LevelAxle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications. They are seeking a Senior Biomedical Imaging Engineer to lead the migration of imaging logic into a modular Nextflow ecosystem, ensuring scientific decision-making at a global scale.
BiotechnologyHealth CareInformation TechnologySoftware
Responsibilities
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)
Qualification
Required
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
Preferred
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
Benefits
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)
Flexible Spending Accounts: Parking Reimbursement Account (PRK)
Flexible Spending Accounts: Dependent Care Assistant Program (DCAP)
Flexible Spending Accounts: Transportation Reimbursement Account (TRN)
Company
Axle
At Axle, we are driven by the mission to accelerate discovery and enhance organizational outcomes by revolutionizing operations with our innovative solutions.
Founded in 2002
501-1000 employees
H1B Sponsorship
Axle has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
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Trends of Total Sponsorships
2025 (37)
2024 (40)
2023 (61)
2022 (30)
2021 (19)
2020 (38)
Funding
Current Stage
Late StageLeadership Team
Gary Mays
Chief Operating Officer
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