E11 Bio - Scientist, Light Sheet Microscopy
Convergent Research
Alameda, CA, USA
USD 96k-165k / year + Equity
Posted on Feb 11, 2026
E11 is working to scale light-microscopy–based connectomics to the whole mouse brain. Our goal is to generate best-in-class, brain imaging datasets that enable rapid and multi-modal reconstruction of neural connectivity. E11 Bio is a non-profit focused research organization organized under the Convergent Research umbrella and located in Alameda, California. We are pursuing ambitious neuroscience research and operating like a nimble start-up while organized as a non-profit. Read our technology roadmap for more.
We are seeking an expert in light-sheet microscopy and large-volume imaging of optically cleared tissue to scale our imaging systems. In addition we are interested in increasing the information extracted per voxel through approaches such as combinatorial molecular encoding, spectral multiplexing, and multi-round readout strategies.
Responsibilities
- Design, build, optimize and maintain lightsheet fluorescence microscopy systems for fast, high-resolution imaging of large connectomics datasets
- Integrate lightsheet microscopy into E11’s optical connectomics platform, co-optimizing hardware, software, and methods for rapid large-scale acquisitions
- Develop, maintain, and extend software solutions for large scale microscope acquisitions including QC and automated responsive controls
- Develop hardware methods for multispectral detection of protein-based cellular barcodes and molecular markers in optically cleared and expanded brain tissue
- Work closely with experimental and computational scientists to collaboratively design experiments, analyze experimental data, and interpret results.
- Collaborate on data collection with scientists developing spatial transcriptomics and proteomics solutions
- Maintain excellent laboratory notebook practices, prepare reports and manuscripts, and present results internally and externally.
Requirements
- PhD in engineering, physics or biology (e.g. biophysics, bioengineering, optical physics) or a related field in science and/or engineering, or equivalent working experience and track record.
- Hands-on experience with building, maintaining and troubleshooting optical microscopes, especially for large-scale, high-throughput, multi-channel acquisitions
- Experience developing cutting-edge optical microscope modalities, such as light-sheet microscopy
Preferred qualifications
- Experience developing methods for optical detection and decoding of multiplexed spatial proteomics information
- Experience with developing and integrating liquid handling, automation and fluid manipulation methods (e.g. microfluidics) with microscopy
- Experience developing optical clearing and/or expansion microscopy
- Experience working directly with computational scientists
- Experience with multichannel image analysis experience
- Experience with adaptive hardware/ software control and smart microscopy
Who Will Love This Job
- You are passionate about neuroscience tool development, and want to broadly accelerate science through long-term commitment to a high-impact project with a tight-knit team.
- You have a strong desire and intrinsic motivation to work collaboratively and inclusively as part of an interdisciplinary team science effort.
- You are committed to the ethos of open science, and want to see your work transparently disseminated.
- You’re mission-driven, and are seeking an environment where you can take long-term risks on moonshot science, shielded from academic or for-profit incentives.
- You’re seeking a high-leverage, non-traditional opportunity to maximize the impact of your science, establishing relationships with key stakeholders in the neuroscience community.
- You understand, appreciate and are ready to tackle the significant experimental challenges to scalable circuit architecture mapping.
We Offer
- An opportunity to help change the world and work with a world-class interdisciplinary team of scientists and engineers on a field-defining moonshot
- Excellent medical, dental, and vision insurance through a PPO plan; parental leave.
- Generous time off + paid holidays.
- Ample healthy and energizing food including daily lunches.
- Wellness allowance 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.
96000 - 165000 USD a year
Base salary range: 96k - 165k
Bonus: Performance-based, up to 20% of base salary
401k match: up to 6% of base salary
Total potential compensation range: 121k - 207k