In Vivo Connectomics Scientist - End-to-End Sample Prep

Convergentresearch; Alameda (CA); On-site; USD 120,000 - 180,000; Full time

Benefits offered by this job

Excellent medical, dental, and vision"

Parental leave

401K matching up to 6%

Daily lunches

Wellness stipend

Job summary

E11 Bio is seeking a mission-aligned experimental scientist for end-to-end sample preparation in connectomics. You will work across bench, microscope, and quantitative analysis with a focus on quality control and protocol optimization.

Collaboration with molecular biology, imaging, and computational teams will drive scalable workflows toward whole-brain connectomics. Strong emphasis on reproducibility and rigorous data handling.

Qualifications

• Ph.D. in neuroscience, biology, bioengineering, or related field, or Ph.D.-equivalent working record.
• 3–5 years of relevant research experience with end-to-end experimental ownership.
• 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 image-analysis workflows (e.g. Python scripts, Fiji macros).
• Strong organizational, documentation, and reproducibility practices.
• Excellent communication and collaboration across wet-lab, imaging, and computational teams.

Responsibilities

• Ensure end-to-end quality across the in vivo sample preparation pipeline, collaborating with technicians, tissue processing, and readiness for imaging.
• Perform stereotaxic injections and perfusions to optimize the pipeline and drive protocol improvements.
• Routinely evaluate injection and perfusion outcomes through microscopy and image analysis.
• Define and maintain sample quality rubrics and ensure consistent scoring over time.
• Develop and maintain image-based workflows to generate quantitative QC metrics with wet lab and computational staff.
• Design experiments to improve sample quality for downstream applications.

Skills

Experimental ownership

In vivo sample prep

Microscopy analysis

Image analysis workflows

Communication & collaboration

Documentation & reproducibility

Education

PhD in neuroscience or related field

Tools

Python

Fiji

Job description

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.

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

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

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

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.

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.