Image Data 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 and enthusiastic image data scientist to develop new methods and tools for processing large-scale next-gen brain microscopy imaging data. You will run the image processing and quality control pipelines while working closely with the computation and wet lab science teams.

Responsibilities

• Develop new methods and tools for processing large-scale next-gen brain microscopy imaging data
• Deploy and optimize developed pipelines in large-scale cluster or cloud environments, ensuring efficient processing and scalability for imaging volumes exceeding petabyte-scale
• Develop robust quality control (QC) analysis tools for anomaly detection, assessing image integrity, and ensuring the accuracy and consistency of generated continuous imaging volumes
• Working closely with wet lab and microscopy scientists to optimize data analysis and acquisition processes
• Engaging in a culture of excellent documentation, preparation of reports, and presenting results internally and externally
  
  

Required Qualifications

• PhD in computer vision, quantitative biology (e.g. biophysics, bioengineering) or a related field in science and/or engineering, or equivalent working experience and track record
• Relevant work or research experience, with strong history of independent and autonomous execution on hard image processing problems
• Strong background in applying computer vision tools to the analysis of large (light) microscopy data
• Experience with software engineering best practices (e.g. version control, code reviews, etc.)
• Excellent communication and collaboration skills, record keeping ability, and attention to detail
  
  

Preferred Qualifications (not Required)

• Experience with computational techniques for stitching and registering microscopy images into volumetric datasets, including handling volume distortions, signal inconsistencies, and other large-scale alignment challenges
• Experience with processing big data in the cloud (e.g. AWS or GCP)
• Familiarity with Zarr data structures and the use of distributed processing tools such as Dask.
• Experience with large scale connectomics data and tools (e.g. Neuroglancer, CATMAID, Knossos, CAVE, or equivalent)
• Familiarity with Nextflow, or other workflow orchestration languages and tools
  
  

Who Will Love This Job

• You are passionate about moonshot neuroscience, and want to broadly accelerate science through long-term 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’re mission-driven, and are seeking an environment where you can take long-term risks on moonshot science, shielded from academic or for-profit incentives.
• You’re seeking a high-leverage, non-traditional opportunity to maximize the impact of your science, establishing relationships with key stakeholders in the neuroscience community.
  
  

$100,000 - $160,000 a year

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.