Scientist, Multiplexed Expansion Microscopy



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Alameda, CA, USA
Posted on Thursday, December 21, 2023
E11 Bio is on a mission to make single-cell brain circuit mapping a routine part of every neuroscientist's toolbox. 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 whitepaper and learn more.
E11 Bio is seeking a creative and passionate scientist to co-develop next-generation technology for molecular connectomic imaging. As a core member of the E11 team, you’ll develop innovative methods for super-resolution multiplexed imaging of cellular morphology and molecular composition at the scale of mammalian brains. Working closely with world experts in cellular barcoding and molecular connectomic data science, you’ll design experiments, collect data, and analyze, interpret, present and publish scientific results consistent with our commitment to open and accessible science for public benefit.


  • Flexibly contribute to the Read team at E11 Bio both in (1) multiplexing data acquisition and (2) multiplexing development work, adapting quickly to shifting priorities aimed at maximizing data acquisition throughput across the whole team.
  • Execute collaborative experiments aimed at acquiring key multiplexing data for E11 Bio’s Year 2 milestones, adapting as needed to circumstances.
  • Perform multiplexing data acquisition, as detailed below.
  • Reliably produce high-quality samples by embedding brain tissue slices into expandable and non-expandable hydrogels.
  • Perform multiplexing experiments on these samples, across all stages of the experiment loop (immunostaining, antibody stripping, imaging).
  • Perform highly accessible documentation and timely data hand-over.
  • Perform multiplexing development work, as detailed below (subject to change according to arising needs).
  • Develop and implement protocols for homogenous penetration of affinity probes into expanded hydrogel/tissue hybrids.
  • Pilot variations of re-embedding protocols, with the goal of improving sample stability during the multiplexing experimental loop.
  • Implement strategies of sample-based non-computational imaging volume registration for multiplexing in expansion microscopy (e.g. GelMap).
  • Develop and implement highly scalable proteomics multiplexing and signal amplification strategies, based on DNA-conjugated affinity probes (e.g. SUM-PAINT or FLASH-PAINT).
  • Operate lab automation systems established at E11, scope future requirements, and interact with external partners to drive their implementation forward.
  • Work closely with experimental and computational scientists to collaboratively design experiments, analyze experimental data, and interpret results.
  • Maintain excellent laboratory notebook practices, prepare reports and manuscripts, and present results internally and externally.
  • Pro-actively source and adapt techniques and methodologies from the literature and scientific community.

Required Qualifications

  • Excellent team science abilities. This includes excellent communication skills that allow the candidate to interface with other team members as needed to hand over or solicit data.
  • Excellent ability to keep accessible records and documentation to make data hand-over and information flow smooth and frictionless within a team.
  • PhD in biology (e.g. biophysics, bioengineering, molecular biology) or a related field in science and/or engineering, or equivalent working experience and track record.
  • Extensive experience with molecular biology laboratory techniques (e.g. cell and tissue culture, optical microscopy, immunohistochemistry, etc.).
  • Experience with methods/protocol development, with emphasis on expansion microscopy and immunohistochemistry.
  • Extensive experience working with cutting-edge optical microscope modalities, such as spinning-disc confocal or light-sheet microscopy.
  • A documented record in experimental innovation, in particular regarding approaches that improve data acquisition throughput (both quantitatively and qualitatively).

Preferred qualifications

  • Experience developing multiplexed spatial proteomics methods (e.g. via antibody stripping or DNA-barcoded antibodies).
  • Experience developing optical clearing and/or expansion microscopy methods.
  • Strong record of publications in peer reviewed scientific journals.

Who will love this job

  • You are passionate about tool development for applications in connectomics, and want to broadly accelerate science through 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 are mission-driven, and are seeking an environment where you can take risks on moonshot science, shielded from academic or for-profit incentives.
  • You are 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 change the world and work with some of the most talented and collaborative experts across scientific fields.
  • Excellent medical, dental, and vision insurance through a PPO plan; parental leave.
  • Generous time off + paid holidays.
  • Wellness allowance for fitness and wellness activities.
We aim to help fill a structural gap in today's R&D system. We enable fundamental research that requires unusual levels of scale and coordination yet is not rapidly monetizable by industry. We’re bringing together top talent from academia, industry, and startups to build a new model for innovative R&D. As an incubator within the Schmidt Futures Network, we identify high-impact scientific or technical research and development opportunities, ultimately defining and launching these projects as Focused Research Organizations.
We are 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 characteristic protected by applicable local, state, or federal law or company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.

This job is no longer accepting applications

See open jobs at [C]Worthy.