Axle Informatics

Senior Biomedical Imaging Engineer

Axle Informatics

full-time

Posted on:

Location Type: Remote

Location: Remote • 🇺🇸 United States

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Job Level

Senior

Tech Stack

CloudDockerGoogle Cloud PlatformLinuxPostgresUnix

About the role

  • 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).

Requirements

  • 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.
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), Parking Reimbursement Account (PRK), Dependent Care Assistant Program (DCAP), Transportation Reimbursement Account (TRN)

Applicant Tracking System Keywords

Tip: use these terms in your resume and cover letter to boost ATS matches.

Hard skills
NextflowDeep Imaging Data AnalysisImage Analysis AlgorithmsHCS Data StructuresLinux/UnixHPC SchedulersNvidia GPU ArchitecturesDockerSingularityQC Metrics
Soft skills
Passion for EngineeringScientific MindsetCollaborationModular DesignStateless Design