E11 bio - scientist i/ii - advanced imaging

E11 Bio is on a mission to advance connectomics towards the scale of whole mammalian brains. We are a collaborative and interdisciplinary team of scientists and engineers engaged in a neuroscience moonshot project to develop a radical technology platform for scalable brain mapping. E11 Bio is a non-profit Convergent Research focused research organization located in Alameda, California, pursuing blue-skies neuroscience research yet operating like a nimble, tight-knit start-up. Read our technology roadmap.

We are seeking a mission-aligned Imaging Scientist to develop, optimize and scale light microscopy workflows for large-scale image acquisition. This role combines sample preparation, advanced microscopy, quantitative image analysis, and engineering-driven technology development with the goal of improving imaging quality and robustness.

You will optimize sample mounting and acquisition strategies, automation, and instrument performance to improve throughput, reproducibility, and data quality at scale. The role will also involve defining quantitative imaging QC metrics, troubleshooting acquisition bottlenecks, and evaluating new hardware and microscopy approaches that can increase imaging capacity. Working closely with sample preparation, molecular biology, hardware, and computational teams, you will help translate experimental requirements into reliable and scalable imaging workflows.

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
• Contribute to improving 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

About you

You have a strong cross-functional mindset with the ability to bridge biological questions and the physical principles of microscopy. You approach technical challenges with curiosity, persistence, and a systematic troubleshooting mindset. You are methodical in documenting experiments, failures, and troubleshooting steps, enabling continuous learning and improvement. You are a dedicated team player who is willing to take on essential tasks to support the team’s success.

Required qualifications

• MSc or PhD in biology, physics or engineering (bioengineering, biomedical engineering, physics, optics, neuroscience, or a related field) or equivalent experience
• Extensive experience with fluorescence microscopy (confocal and spinning-disk microscopy)
• Strong experimental skills and ability to troubleshoot imaging, sample or instrument-related issues
• Familiarity with fluorescence labeling, fluorophore selection, as well as sample preparation and mounting workflows
• Comfort with the 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 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

Preferred qualifications

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

Outcomes

In the first 6 months you will:

• Develop a strong working knowledge of our microscopy systems, independently operate them, and train other users
• Become a key point of contact for troubleshooting and day-to-day support of commercial microscopy systems
• Reduce microscope downtime by taking ownership of routine quality control and performance checks for imaging systems
• Learn and apply standard sample preparation and mounting workflows
• Get a deep technical understanding of E11’s end-to-end acquisition workflows

In the first 12 months you will:

• Routinely perform reliable, reproducible acquisition workflows across multiple imaging systems
• Improve image quality, acquisition robustness and throughput through systematic optimization of imaging parameters
• Develop and validate improved sample mounting, fluorophore and imaging buffer strategies for long-duration acquisition
• Implement stronger QC and performance benchmarking to surface 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

An opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields. An opportunity to gain experience on a field-defining moonshot effort. Excellent medical, dental, and vision insurance through a PPO plan; parental leave. Generous time off + paid holidays. 401K matching up to 6% of base salary. Ample healthy and energizing food including daily lunches. Stipend for fitness and wellness activities.

E11 Bio, LLC is an Equal Employment Opportunity employer that proudly pursues and hires a diverse workforce. We do not make hiring or employment decisions on the basis of race, color, religion or religious belief, ethnic or national origin, nationality, sex, gender, gender-identity, sexual orientation, disability, age, military or veteran status, or any other basis protected by applicable local, state, or federal laws or prohibited by Company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.