E11 Bio - Scientist, Tissue & Imaging Quality

E11 Bio is a Focused Research Organization (FRO) with a long-term mission to make connectomics scalable and cost-effective for mammalian brains – first for mice and eventually for humans.

We have recently developed PRISM, a platform technology for low cost optical connectomics. PRISM integrates advances in genetic cell barcoding, multiplexed expansion microscopy, and machine-learning based -based spatial reconstruction to solve key bottlenecks in data acquisition and analysis. PRISM will reduce the cost of connectomics 100-fold and thereby transform neuroscience, treatments for brain disorders, and neuro-inspired computing.

E11 Bio is seeking a mission-aligned experimental scientist who is equally comfortable at the bench, the microscope, and with quantitative data analysis. This role is responsible for sample preparation end-to-end for high-quality connectomics, combining hands-on experimental work with quantitative image-based QC to diagnose failure modes and iteratively improve protocols. You will collaborate closely with molecular biology, imaging, and computational teams to ensure we consistently prepare high quality specimens and brain tissue to support our ambitious scaling goals towards whole-brain connectomics.

Core Responsibilities:
• Ensure consistent end-to-end quality across our in vivo sample preparation pipeline. Collaborate with technicians, including viral delivery and animal perfusion, tissue processing, and overall readiness for imaging and molecular readouts
• Perform and troubleshoot stereotaxic injections and perfusions as needed to optimize our in vivo sample preparation pipeline and guide protocol improvements
• Routinely evaluate injection and perfusion outcomes (viral labeling, tissue quality, use for downstream work) through microscopy and image analysis
• Define, implement, and maintain sample quality rubrics (e.g. labeling density, barcode density) and ensure samples are scored consistently over time
• Develop and maintain image-based workflows to generate quantitative QC metrics based on partnership and feedback with wet lab and computational staff
• Design and perform experiments to improve sample quality when it is limiting for downstream applications
• Extend quality assessment to RNA integrity and molecular preservation

Required Qualifications:
• Ph.D. in neuroscience, biology, bioengineering, or a related life-science or engineering field, or Ph.D.-equivalent working record
• 3–5 years of relevant research experience with a strong track record of end-to-end experimental ownership
• Demonstrated hands-on experience with in vivo sample preparation, including stereotaxic injections, perfusions, and tissue handling
• Experience acquiring and working with confocal and widefield microscopy data
• Experience developing or maintaining fit-for-purpose image-analysis workflows (e.g. Python scripts, Fiji macros, or equivalent) to support experimental iteration
• Strong organizational, documentation, and record-keeping practices and strong attention to reproducibility
• Excellent communication and collaboration skills, particularly across wet-lab, imaging, and computational teams

Preferred Qualifications:
• Experience designing or applying quality control rubrics or scoring systems for biological samples or imaging data
• Familiarity with image-analysis pipelines for cell counting, morphology, spatial distributions, or intensity-based metrics
• Experience working in highly iterative or startup-like research environments and in work where roles span multiple technical domains

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.