Software Engineer - Royer Group

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Join the Chan Zuckerberg Biohub San Francisco: Software Engineer Opportunity

The Chan Zuckerberg Biohub San Francisco (CZ Biohub SF) is a pioneering, independent nonprofit research institute. We unite the expertise of Stanford, UC Berkeley, and UC San Francisco to fuel innovative technology and groundbreaking discoveries. Our mission is to support top-tier engineers, data scientists, and biomedical researchers in uncovering the mechanisms of disease and developing revolutionary diagnostics and therapies. Our values emphasize scholarly excellence, disruptive innovation, hands-on engineering, collaboration, open communication, inclusiveness, and equal opportunity for all.

Our Vision

  • We tackle significant scientific challenges that conventional settings cannot address.
  • We empower individual researchers to pursue their most audacious and innovative ideas.
  • Our technologies facilitate research efforts for scientists and clinicians both within our partner institutions and globally.

Commitment to Diversity and Inclusion

At CZ Biohub SF, diversity of thought, ideas, and perspectives is paramount. We are dedicated to fostering an inclusive environment where every team member feels valued and their contributions are acknowledged.

The Opportunity: Software Engineer I

As a Software Engineer I, you will be responsible for maintaining a cutting-edge software suite for large-scale light-sheet image storage, processing, analysis, and visualization. Using the latest technologies and libraries—such as napari, Cupy, Dask, Zarr, scikit-image, PyTorch, and more—you will play a vital role in our research initiatives. Ideal candidates will have familiarity with open-source cell tracking software Ultrack, a solid grasp of multi-dimensional developmental imaging, particularly light-sheet microscopy, and a passion for open-source software and community building.

Responsibilities

  • Innovate and develop highly efficient methods for 3D cell segmentation and tracking of large-scale light-sheet microscopy data.
  • Author and publish research papers in top-tier journals and conferences.
  • Create, document, and maintain impactful open-source software for image analysis of light-sheet microscopy datasets.
  • Collaborate with cross-functional teams on top-level projects at CZ Biohub.
  • Assist both internal and external teams in utilizing our software tools effectively.
  • Strengthen ties to upstream projects including napari, zarr, dask, and scikit-image.
  • Collaborate within the CZ ecosystem, including CZI, CZII, CZB Chicago, and CZB New York.

Qualifications

Essential

  • Master’s degree in Computer Science (completed or nearing completion), ideally specializing in Computer Vision, Deep Learning, and AI.
  • 3+ years of experience in coding and developing image processing and analysis pipelines.
  • 6+ years of software engineering experience.
  • Proficiency in professional software development concepts and tools.
  • Experience programming in languages such as C/C++, Java, Python, OpenCL, and CUDA.
  • Experience with managing multi-terabyte datasets.
  • Fluorescence imaging experience.
  • Proven track record of writing academic manuscripts.
  • Familiarity with libraries such as Numpy, SciPy, Dask, Cupy, Numba, scikit-image, and napari.
  • Expertise in image processing for microscopy and deep learning model design in Tensorflow or PyTorch.
  • Relevant independent research experience.

Please note that all employees, contractors, and interns at the Chan Zuckerberg Biohub are required to present proof of full COVID-19 vaccination, including a booster dose if eligible, by their start date. Exceptions are available for individuals due to disabilities or sincerely held religious beliefs.

Compensation

Annual salary range: $92,000 - $126,500

What We Provide

  • Resources to drive innovative biology and disease research.
  • A collaborative environment with diverse expertise.
  • Access to CZ Biohub's technology platforms and research group leaders.
  • Collaborative opportunities with Stanford, UC Berkeley, and UC San Francisco.
  • Competitive salary and benefits, commensurate with experience.

Benefits

Our comprehensive benefits program supports the invaluable work