Data Scientist II: Deep Learning for 3D Microscopy (Remote-Eligible)

ClearCompany Talent Management Software; Seattle, Northern (WA, KY); Hybrid; USD 113,000 - 140,000; Full time

Job summary

The Allen Institute is seeking a Data Scientist II to advance deep learning and image analysis for 3D microscopy timelapse data. You will build and optimize end-to-end ML/DL pipelines, collaborate with experimental and computational scientists, and deploy scalable methods on HPC infrastructure.

The role emphasizes reproducible workflows, code quality, and staying current with ML advances. Onsite with limited remote work, focusing on open science and collaborative discovery.

Qualifications

• Bachelor's degree in computer science, engineering, physics, data science, computational biology, or a related quantitative field.
• 1+ year of relevant experience.
• Proficiency in Python, including scientific and data manipulation libraries (e.g. NumPy, scikit-image).
• Working experience with a deep learning framework such as PyTorch or TensorFlow.

Responsibilities

• Design and implement ML/DL pipelines for microscopy image analysis, in collaboration with senior data engineers and scientists.
• Preprocess and clean large-scale microscopy datasets, ensuring data quality and integrity for downstream analysis.
• Develop, optimize, and fine-tune models for segmentation, feature extraction, and classification.
• Integrate and scale image analysis protocols into high-throughput computational pipelines with cross-functional teams.
• Participate in code reviews and contribute to maintainable, well-documented codebases.
• Maintain reproducible analysis records; version-controlled code, documented parameters, and traceable results.
• Track developments in ML and image analysis; evaluate methods against our data.
• Adherence to SOPs, GLPs and regulatory requirements.

Skills

Python

NumPy

scikit-image

Deep learning

Education

Bachelor's degree in Computer Science or related field

Tools

PyTorch

TensorFlow

Job description

The Allen Institute is seeking a Data Scientist II to advance deep learning and image analysis for 3D microscopy timelapse data. You will build and optimize end-to-end ML/DL pipelines, collaborate with experimental and computational scientists, and deploy scalable methods on HPC infrastructure.

The role emphasizes reproducible workflows, code quality, and staying current with ML advances. Onsite with limited remote work, focusing on open science and collaborative discovery.