"Assistant/Associate/Full Project Scientist - Machine Learning & Data Analytics Advanced Bioimaging Center Department of Molecular and Cell Biology"

The Advanced BioImaging Center (ABC) in the Department of Molecular and Cell Biology at the University of California, Berkeley seeks applications for two Project Scientists at the Assistant, Associate, or full rank. The selected candidate will be appointed at the rank commensurate with prior experience. The position will report to Professor Gokul Upadhyayula, with Professor Eric Betzig serving as an additional academic mentor. The project scientist will make significant and creative contributions in the area of machine learning & data analytics.

The Advanced BioImaging Center (ABC) at UC Berkeley aspires to be a world-leading multidisciplinary imaging center that drives important biological discoveries through critical new advances in all aspects of imaging technology and that drives the dissemination of that technology through a multi-pronged education strategy to scientists around the world. ABC was intentionally designed to maximize scientific productivity and impact by adopting groundbreaking imaging technologies such as the next-generation adaptive optical multifunctional microscope, incorporating the high-level technical expertise of instrumentation scientists, applied mathematicians, and computational scientists, and building worldwide collaborations aimed at tackling the challenges posed by terabyte and petabyte-scale imaging data processing, visualization, and dissemination. Members of the ABC have access to leading-edge imaging and computing hardware, as well as exposure to collaborators from a range of diverse disciplines, including in the fields of Artificial Intelligence, Data Science, Mathematics, and more.

The Assistant/Associate/Full Project Scientists will be an integral part of a visionary scientific team driving cutting-edge biological discoveries through immediate applications of critical advances in imaging technologies. These positions will work with a dedicated team to develop data analytics software in terabyte- to petabyte-scale imaging projects. The incumbents will develop and refine machine learning applications and manage projects and provide regular progress reports to PIs and collaborators.

Successful candidates will be an integral part of the expert team working together with computational scientists and biologists in experimental design to tackle complex biological questions in a quantitative manner. The work will primarily be conducted at the facility in Barker Hall. Occasional travel may be required.

Key Responsibilities:

• Make significant and creative contributions to development of new imaging and data processing tools for datasets generated on multicellular tissues, organoids, transparent embryos.
• Design, build, and maintain new software packages for efficient data processing.
• Advise on applications of these tools for biological imaging; collaborate with Postdocs and graduate students on specific projects to test, learn and implement for general and specific use cases.
• General organization and management of software documentation.
• Bring cross disciplinary expertise to solve problems at the intersection between life science, computer vision, and state-of-the-art AI methods.
• Work with petabyte-scale light sheet datasets that are typically 4D or 5D (x,y,z,t,chemistry). Identify and implement scalable solutions to scientific questions on large-scale data sets, especially using performant algorithms.
• Develop machine learning approaches, computer vision tools to help pre-process dataset and annotations to generate groundtruth benchmarks.
• Contribute to dissemination via open source code repositories, demonstrations, publications, presentation.

These positions will be eligible for full benefits.

Lab: https://abc.berkeley.edu/

Contract: https://uaw5810.org/ar-contract-2022/

Qualifications:

Basic qualifications (required at time of application): PhD (or equivalent international degree).

Additional qualifications (required at time of start): For the Assistant Project Scientist rank: 4+ years of postdoctoral research experience; For the Associate Project Scientist rank: 8+ years of post PhD research experience; For the full Project Scientist rank: 14+ years of post PhD research experience.

Preferred qualifications: PhD or equivalent international degree in Computation Data, Computer Sciences, Bioinformatics or Related field; Demonstrated record of productivity and publications and/or scholarly contributions; Strong biological background and understanding of molecular biology; Demonstrate understanding of optical microscopy, including light sheet microscopy, adaptive optics, and modern scientific cameras; Demonstrated ability to work in a research team, manage active collaborations with other academic groups; Demonstrated experience handling and processing large scale imaging datasets (>100TB to petabyte scale and beyond); Expertise in programming in C++, Labview, MATLAB, Python; Expertise in databases, data infrastructure, data governance; Expertise in high performance computing using SLURM or LSF; Experience with PyTorch, JAX, or Tensorflow; Experience with NVIDIA CUDA and related OpenMP programming; Experience with cloud services (AWS, GCP, Azure, etc); Experience with state of the art AI/ML architectures (vision transformers, diffusion models, etc); Experience mentoring undergraduate/graduate students, and/or technicians; Experience with professional speaking engagements; Ability to effectively communicate, participate in efficient and open collaboration, and engage with a diverse group of researchers; The ideal candidate will be innovative and able to synergize various ideas and approaches, while exercising sound judgment to evaluate and take acceptable risks.

Application Requirements: Document requirements: Curriculum Vitae; Cover Letter; Statement of Research; Project Portfolio; Statement on Contributions to Diversity, Equity, Inclusion, and Belonging. Reference requirements: 3-5 required (contact information only). Apply link: https://aprecruit.berkeley.edu/JPF04705. Help contact: harrisonmd@berkeley.edu.