E11 Bio - Scientist I/II, Expansion Microscopy

Convergent Research; Alameda (CA); On-site; USD 100,000 - 170,000; Full time

Benefits offered by this job

Health insurance

Parental leave

Paid time off

401K match

Daily lunches

Wellness stipend

Job summary

E11 Bio in Alameda, California seeks a mission-aligned scientist/engineer for expansion microscopy development and protocol optimization within our production pipeline. You will drive gel performance, QC metrics, and scalable sample production while collaborating with molecular biology, imaging, and computational teams.

The role blends hands-on bench work with quantitative analysis, protocol automation, and cross-disciplinary collaboration to advance toward whole-brain connectomics.

Qualifications

• Ph.D. in biology, chemistry, bioengineering, materials science, mechanical engineering, or related field, or equivalent research/industry experience.
• Strong end-to-end experimental ownership demonstrated.
• Experience with hydrogel chemistry, expansion microscopy, immunohistochemistry, or tissue processing.
• Excellent communication and reproducibility practices.

Responsibilities

• Independently design, coordinate, and execute bench-level expansion microscopy experiments.
• Maintain high-quality gels within the production pipeline.
• Iteratively optimize workflows by sourcing methods from literature.
• Pilot variations to improve signal retention across multi-round cycles.
• Explore diffusion improvements and collaborate with vendors for devices.
• Collaborate with experimental and computational teams to design and analyze experiments.
• Document results and assist in manuscripts and reports.

Skills

Experimental ownership

Communication & collaboration

Quantitative data analysis

Education

Ph.D. in biology/chem/bioengineering

Tools

Spinning-disc confocal microscopy

Light-sheet microscopy

Automation (Arduino/ Raspberry Pi)

Python scripting

Job description

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 scientist or engineer who is equally comfortable at the bench, the microscope, and with quantitative data analysis. This role combines sample preparation, advanced microscopy, quantitative image analysis, with engineering-driven technology development focused on quick iterative troubleshooting and standardizing and automating protocols. You will collaborate closely with molecular biology, imaging, and computational teams to ensure we consistently prepare high quality specimens to support our ambitious scaling goals towards whole-brain connectomics.

The role forms a critical part of our sample production pipeline and will be responsible for expansion microscopy development and iteratively improving protocols. Your work will drive two overarching outcomes: improving gel performance and improving the quality, reproducibility and scalability of sample production. This combines hands-on experimental work with defining quantitative metrics to assess mechanical and optical gel properties, image quality and pipeline throughput.

Responsibilities

• Independently design, coordinate, and execute bench level experiments focused on expansion microscopy.

• Operate within our sample production pipeline to ensure a continuous flow of high-quality gels

• Iteratively optimize expansion microscopy workflows by designing, sourcing and adapting techniques and methodologies from the literature and scientific community

• Pilot variations of expansion microscopy protocols focused on optimizing signal retention for multi-round cycles of immunostaining, imaging, and signal extinction.

• Pilot methods for increasing diffusion within expanded hydrogel/tissue hybrids. Pilot commercially available devices (e.g. ultrasound or microwave) and design custom built devices (in collaboration with external vendors) to facilitate these experiments.

• Work closely with experimental and computational scientists to collaboratively design experiments, analyze experimental data, and interpret results.

• Maintain excellent laboratory notebook practices, communicate results through reports and presentations, and contribute to and assist in preparation of manuscripts, abstracts and other scientific documents.

Required Qualifications

• Ph.D. in biology, chemistry, bioengineering, materials science, mechanical engineering, or a related field, or equivalent research or industry experience

• Strong track record of end-to-end experimental ownership.

• Experience developing methods or protocols, ideally involving hydrogel chemistry, expansion microscopy, immunohistochemistry, or tissue processing

• Excellent communication and collaboration skills, with strong record-keeping practices and attention to reproducibility.

Preferred Qualifications

• Experience working with advanced optical microscope modalities (e.g., spinning-disc confocal or light-sheet microscopy).

• Experience designing or applying quantitative scoring systems for expansion microscopy or imaging data

• Experience with scaling expansion microscopy throughput in routine production environments

• Experience automating lab workflows (e.g., liquid handlers, microcontrollers like Arduino or Raspberry Pi, scripting in Python)

Strong engineers new to these techniques are encouraged to apply, as are creative experimentalists from outside neuroscience who have developed expansion microscopy or similar methods in other fields. We’re looking for self-starters that iterate quickly and find creative, practical solutions to complex problems. Experience working in fast paced startup-like research environments where roles span multiple technical domains is preferred.

In 6 months, you will have:

• Fully onboarded into the E11 production pipeline and be consistently generating high-quality gels for imaging

• Identify and standardize expansion microscopy QC metrics (e.g, measuring mechanical or optical properties) and stage gate thresholds, and integrated their routine measurement into the pipeline

• Increased production gel yield by 50% without a reduction in quality

In 12 months, you will have:

• Improved the quality, reproducibility, and scalability of the pipeline, both in throughput and in the physical sample sizes we can process (for example, by developing methods for high-quality whole-brain gelation and expansion)

• Increased the reproducibility of our protocols so that technical variability between and within samples processed in parallel is reduced by 50%

• Reduced hands-on protocol time while improving outcomes and reproducibility, for example through in-house automation development or automation partnerships.

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.

• 401K matching up to 6% of base salary

• Ample healthy and energizing food including daily lunches.

• Stipend for fitness and wellness activities.

$100,000 - $170,000 a year

Base salary range: $100,000 - $170,000 a year

Bonus: Performance-based, up to 20% of base salary

401K match: 6%

Total potential compensation: $125,000 - $214,000

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.