E11 Bio - Scientist I/II - Advanced Imaging

Convergent Research•Alameda, CA

5d•Onsite

About The Position

E11 Bio is a non-profit Convergent Research focused research organization in Alameda, California, working to advance connectomics toward mapping whole mammalian brains. The Scientist I/II will develop, optimize, and scale light microscopy workflows for large-scale image acquisition. The role combines sample preparation, advanced microscopy, quantitative image analysis, and engineering-driven technology development to improve imaging quality and robustness. The scientist will optimize sample mounting and acquisition strategies, automation, and instrument performance to improve throughput, reproducibility, and data quality at scale. The position also involves defining quantitative imaging quality-control metrics, troubleshooting acquisition bottlenecks, and evaluating hardware and microscopy approaches that could increase imaging capacity. The scientist will work across sample preparation, molecular biology, hardware, and computational teams to translate experimental requirements into reliable, scalable imaging workflows. The successful candidate will develop expertise in E11 Bio’s microscopy systems and acquisition workflows, support routine operations and user training, and improve image quality, throughput, automation, and instrument reliability over time.

Requirements

MSc or PhD in biology, physics, or engineering (including bioengineering, biomedical engineering, physics, optics, or neuroscience, or a related field), or equivalent experience.
Extensive experience with fluorescence microscopy, including confocal and spinning-disk microscopy.
Strong experimental skills and ability to troubleshoot imaging-, sample-, or instrument-related issues.
Familiarity with fluorescence labeling, fluorophore selection, sample preparation, and mounting workflows.
Comfort with acquisition, visualization, and basic analysis of large imaging datasets.
Ability to follow, document, and improve technical protocols and standard operating procedures.
Strong organizational and communication skills, with the ability to work effectively across experimental, computational, and engineering teams.
Ability to learn new instrumentation and workflows quickly and work increasingly independently over time.
Strong cross-functional mindset and ability to bridge biological questions with the physical principles of microscopy.
Curiosity, persistence, and a systematic approach to troubleshooting technical challenges.
Methodical documentation of experiments, failures, and troubleshooting steps.
Team-oriented approach and willingness to take on essential tasks in support of team success.

Nice To Haves

Experience handling and imaging cleared or expanded biological specimens.
Experience performing and optimizing high-throughput, long-duration, or automated microscopy acquisitions.
Experience operating, maintaining, and troubleshooting custom or advanced microscopy systems.
Programming experience and/or proficiency applying computational tools, including AI or machine learning, to automate workflows, analyze microscopy data, or improve imaging performance.

Responsibilities

Perform routine quality control and performance benchmarking of five or more imaging systems.
Serve as the point of contact for microscope maintenance, troubleshooting, and user onboarding.
Execute high-throughput imaging acquisitions and support day-to-day acquisition operations.
Improve end-to-end acquisition workflows, including instrument configuration, acquisition parameter optimization, and automated imaging routines.
Optimize fluorophore and imaging buffer selection to enhance signal intensity and imaging robustness.
Test and refine sample mounting approaches for reliable long-duration acquisitions.
Collaborate with image data scientists, vendors, and contractors to facilitate, co-develop, and integrate custom hardware and software solutions.
Develop working knowledge of microscopy systems, operate them independently, and train other users.
Take ownership of routine quality control and performance checks to reduce microscope downtime.
Apply standard sample preparation and mounting workflows and build technical understanding of end-to-end acquisition workflows.
Improve image quality, acquisition robustness, and throughput through systematic optimization of imaging parameters.
Develop and validate sample mounting, fluorophore, and imaging buffer strategies for long-duration acquisition.
Strengthen quality control and performance benchmarking to identify hardware and process issues early.
Increase automation and reduce manual intervention in high-throughput acquisition workflows.
Resolve recurring technical bottlenecks and improve day-to-day microscope reliability.
Help integrate new hardware and software capabilities into existing imaging workflows.