Join HHMI’s Foundational Microscopy Image Analysis (MIA) project as a Data Engineer and help build the data backbone for AI-powered spatial biology. You will design, develop, and optimize scalable data pipelines, including multi-node GPU training and inference systems, to support large, heterogeneous microscopy image datasets. Your daily tasks include writing production-quality Python code to parse and validate microscopy data from various sources, ensuring scientific integrity and reproducibility. This role requires expertise in data engineering, high-performance computing environments, and ML frameworks like PyTorch or JAX. You will collaborate with interdisciplinary teams of computational and experimental scientists, maintaining detailed documentation and potentially mentoring junior engineers. The project aims to create one of the world’s most comprehensive multimodal 3D/4D microscopy datasets, driving impactful scientific research in life sciences.
Skills
Python
PyTorch
JAX
Kubernetes
AWS SageMaker
Google Vertex AI
HDF5
Zarr
Parquet
webdataset
Docker
CI/CD
Git
Slurm
LSF
Matplotlib
R
Jupyter notebooks
Cloud-based computing
Multi-node GPU processing
What you'll do
Design and implement scalable data pipelines for foundational microscopy datasets.
Develop multi-node GPU training and inference pipelines for vision foundation models.
Maintain comprehensive documentation of data provenance and transformation steps.
Establish data standards, formats, and workflows to ensure quality and reproducibility.
Analyze large datasets using statistical tools and programming languages like Python and R.
Collaborate with interdisciplinary teams to define best practices in data engineering.
What we're looking for
Bachelor’s degree in Computer Science or related field with 3+ years of data engineering experience.
Experience with volumetric 3D/4D microscopy data analysis tools and high performance compute environments.
Proficiency in distributed data processing, multi-node GPU processing, and ML development frameworks like PyTorch and JAX.
Expertise in building scalable data solutions and ensuring data quality and accessibility.
Strong technical documentation and communication skills for multidisciplinary team collaboration.
Experience with data formats such as Zarr, Parquet, HDF5, and efficient IO methods.
Utilization of data visualization libraries like Matplotlib and proficiency in Python.
Market check
Salary context
This listing doesn't show a salary. Similar roles on FindRole typically pay
$106,560–$187,790.
Peer median band
$106,560–$187,790
Median floor and ceiling across peers.
Typical midpoint (25–75%)
$126,800–$199,850
Middle half of comparable postings.
Based on 240 comparable postings.*
* 240 is the maximum number of comparable postings sampled.
Employer
About Howard Hughes Medical Institute (HHMI)
Howard Hughes Medical Institute (HHMI) is one of the largest private biomedical research organizations in the world, funding basic research and science education to advance human health and knowledge. Industry: Biomedical Research & Science Education
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