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.

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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  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.

• 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

• 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.

• 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

• Experience handling and imaging cleared or expanded biological specimens

• Experience with performing and optimizing high-throughput, long-duration or automated microscopy acquisitions

• Experience operating,…