E11 Bio - Scientist I​/II, Expansion Microscopy

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.

• 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.

• 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.

• 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,…