E11 Bio - Associate Computational Scientist

E11 Bio is on a mission to advance connectomics towards whole brain scale for humans and other mammals. 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 mammalian 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.

E11 Bio is seeking a motivated, mission‑aligned Associate computational scientist to develop, maintain and optimize the workflows and infrastructure that process our large‑scale brain mapping data. You will be responsible for keeping petabytes of imaging data moving reliably from the microscope to finished, processed volumes. That means helping maintain our data pipelines as well as being hands‑on with the physical computing and network infrastructure.

In addition, you will interact daily with biologists and microscopists on frontier research to identify new areas where scientific computing may accelerate their progress. For this you will build solutions that solve real problems at the bench: from quality control and real‑time data analysis to agentic lab automation.

This position is on‑site only, in Alameda, CA.

• Operate and improve automated pipelines that process petabyte‑scale volumetric microscopy data reliably from acquisition to complete volumes
• Maintain on‑prem servers, storage and networking; diagnose and replace failed hardware, assist in coordination with vendors, and support scaling across on‑prem and cloud compute
• Collaborate and coordinate with remote senior engineers to provide fast and reliable hands‑on support
• Work with wet lab scientists to identify, build and own new tools for the lab, from QC processes and live dashboards to simple analysis tools
• Train lab scientists on our software tools and turn their experience into actionable feedback
• Help maintain and extend our pipeline‑wide tracking dashboard to help catch problems early, improve our processes and make data quality visible across the team
• Contribute to our agentic lab automation efforts by taking on projects to set up AI‑driven control of lab instruments, with guidance from senior staff
• Engaging in a culture of excellent documentation, preparation of reports, and presenting results internally and externally

• Bachelor's or Master's in computer science, or another science or engineering field with a computational focus, or equivalent experience.
• Solid software development practices:
  Python, git, testing, documentation.
• Fluent with AI‑assisted, agentic development (e.g. Claude Code, Cursor etc.) as a daily workflow, including directing coding agents and reviewing and testing their output.
• Data science fundamentals: numpy, scipy, and working with large datasets.
• Comfort with Linux administration and computer hardware fundamentals, and a willingness to get hands‑on with physical equipment.
• Strong interpersonal and communication skills, and a real interest in translating between people with very different expertise.
• Curiosity about the brain and an appetite to learn neuroscience on the job.

• Experience with servers, storage, networking fundamentals or IT infrastructure.
• Experience with large‑scale scientific data and ML workflows, especially imaging data.
• Familiarity with HPC, job schedulers, distributed or cloud computing, and containers (Docker/Apptainer).
• Experience working in a wet‑lab or applied lab setting, ideally including software integration of lab hardware, such as writing custom control workflows.
• Experience with reproducible workflows and…