E11 Bio - Scientist I/II - Advanced Imaging

Convergent Research • Alameda, CA

7d • $99,000 - $170,000 • Onsite

About The Position

E11 Bio is a non-profit Convergent Research focused research organization in Alameda, California, developing technology for scalable brain mapping. The Scientist I/II - Advanced Imaging will develop, optimize, and scale light microscopy workflows for large-scale image acquisition. The work 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 role includes defining quantitative imaging QC metrics, troubleshooting acquisition bottlenecks, and evaluating hardware and microscopy approaches that could increase imaging capacity. The scientist will work closely with sample preparation, molecular biology, hardware, and computational teams to translate experimental requirements into reliable, scalable imaging workflows.

Requirements

• MSc or PhD in biology, physics, or engineering (including bioengineering, biomedical engineering, physics, optics, or neuroscience), 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 SOPs.
• Strong organizational and communication skills, with 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 physical principles of microscopy.
• Curiosity, persistence, and a systematic troubleshooting mindset.
• Methodical documentation of experiments, failures, and troubleshooting steps.
• Collaborative team approach and willingness to take on essential tasks to support 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 5+ 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.
• Support troubleshooting and day-to-day operation of commercial microscopy systems.
• Take ownership of routine quality control and performance checks to reduce microscope downtime.
• Learn and apply standard sample preparation and mounting workflows.
• Improve image quality, acquisition robustness, throughput, and microscope reliability through systematic optimization.
• Develop and validate improved sample mounting, fluorophore, and imaging buffer strategies for long-duration acquisition.
• Implement QC and performance benchmarking to identify hardware and process issues early.
• Increase automation and reduce manual intervention in high-throughput acquisition workflows.
• Help integrate new hardware and software capabilities into existing imaging workflows.

Benefits

• Performance-based bonus of up to 20% of base salary.
• 401(k) matching up to 6% of base salary.
• Medical, dental, and vision insurance through a PPO plan.
• Parental leave.
• Generous time off and paid holidays.
• Daily lunches and healthy, energizing food.
• Stipend for fitness and wellness activities.
• Opportunity to work on a field-defining moonshot effort with collaborative experts across scientific fields.

What This Job Offers

• Job Type: Full-time
• Career Level: Entry Level