Senior Biomedical Imaging Engineer
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Job Description
Senior Biomedical Imaging Engineer optimizing imaging pipelines at Axle Informatics. Responsible for pipelines transitioning to modular, cloud-native solutions.
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).
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)
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