Software Engineer - Royer Group
Apply NowCompany: Chan Zuckerberg Biohub - San Francisco
Location: San Francisco, CA 94112
Description:
The Chan Zuckerberg Biohub San Francisco (CZ Biohub SF) (https://www.czbiohub.org/sf/) is an independent nonprofit research institute that brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine. CZ Biohub SF itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.
Our Vision
Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network and enable disruptive innovation and scholarly excellence. We are committed to cultivating an inclusive organization where all colleagues feel inspired and know their work makes an important contribution.
The Opportunity
The Software Engineer I will maintain a software suite for large-scale light-sheet image storage, processing, analysis, and visualization that leverages the latest technologies and libraries, such as napari, Cupy, Dask, Zarr, scikit-image, PyTorch, and more. The ideal candidate will be familiar with the open-source cell tracking software Ultrack and be comfortable with basic concepts in multi-dimensional developmental imaging, in particular with light-sheet microscopy, have experience coding algorithms for image processing with classical as well as deep learning methods, and have demonstrated experience and be passionate about open-source software and community building.
You will
You have
Essential -
The Chan Zuckerberg Biohub requires all employees, contractors, and interns, regardless of work location or type of role, to provide proof of full COVID-19 vaccination, including a booster vaccine dose, if eligible, by their start date. Those who are unable to get vaccinated or obtain a booster dose because of a disability, or who choose not to be vaccinated due to a sincerely held religious belief, practice, or observance must have an approved exception prior to their start date.
Compensation
What We Provide
Benefits
We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world's leading scientists.
The CZ Biohub Network is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.
Pursuant to the California Fair Chance Act, we will consider for employment qualified applicants with arrest and conviction records.
Headhunters and recruitment agencies may not submit resumes/CVs through this website or directly to managers. The CZ Biohub Network does not accept unsolicited headhunter and agency resumes. The CZ Biohub Network will not pay fees to any third-party agency or company that does not have a signed agreement with the CZ Biohub Network.
Our Vision
- We pursue large scientific challenges that cannot be pursued in conventional environments
- We enable individual investigators to pursue their riskiest and most innovative ideas
- The technologies developed at CZ Biohub San Francisco facilitate research by scientists and clinicians at our home institutions and beyond
Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network and enable disruptive innovation and scholarly excellence. We are committed to cultivating an inclusive organization where all colleagues feel inspired and know their work makes an important contribution.
The Opportunity
The Software Engineer I will maintain a software suite for large-scale light-sheet image storage, processing, analysis, and visualization that leverages the latest technologies and libraries, such as napari, Cupy, Dask, Zarr, scikit-image, PyTorch, and more. The ideal candidate will be familiar with the open-source cell tracking software Ultrack and be comfortable with basic concepts in multi-dimensional developmental imaging, in particular with light-sheet microscopy, have experience coding algorithms for image processing with classical as well as deep learning methods, and have demonstrated experience and be passionate about open-source software and community building.
You will
- Devise highly performant & novel approaches for 3D cell segmentation and tracking for large-scale light-sheet microscopy data
- Write and publish manuscripts in top-tier journals and conferences on a regular basis
- Develop, document, and maintain high-impact open-source software for image processing and analysis of light-sheet microscopy datasets
- Collaborate with other groups and platforms on CZ Biohub's top-line projects
- Help internal and external collaborators use our software tools
- Foster existing ties to upstream projects such as napari, zarr, dask, and scikit-image, ...
- Collaborate and synergize with other efforts within the CZ ecosystem (CZI, CZII, CZB Chicago, CZB New York)
You have
Essential -
- Master in Computer Science (completed or soon to be completed), ideally with a specialization in Computer Vision, Deep Learning, and AI
- 3 years of experience coding and developing image processing and analysis pipelines
- At least 6 years of experience in software engineering
- Familiarity with professional software development concepts and tools
- Experience writing code in C/C++, Java, Python, OpenCL, and CUDA
- Experience handling multi-terabyte-sized datasets
- Experience with fluorescence imaging
- Experience writing academic manuscripts
- Experience with libraries such as : Numpy, SciPy, Dask, Cupy, Numba, scikit-image, napari etc.
- Experience with image processing for microscopy
- Experience designing and running deep learning models in Tensorflow or PyTorch Relevant independent research experience
The Chan Zuckerberg Biohub requires all employees, contractors, and interns, regardless of work location or type of role, to provide proof of full COVID-19 vaccination, including a booster vaccine dose, if eligible, by their start date. Those who are unable to get vaccinated or obtain a booster dose because of a disability, or who choose not to be vaccinated due to a sincerely held religious belief, practice, or observance must have an approved exception prior to their start date.
Compensation
- $92,000 - $126,500
What We Provide
- Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease
- A collegial and collaborative environment consisting of diverse expertise
- Existing collaborations within CZ Biohub: Technology Platforms (Bioengineering, Computational Microscopy, Data Science, Genomic Sequencing, Mass Spectrometry/Proteomics), and Research Group Leaders
- Access to collaborators, resources and facilities at our three partner universities (Stanford, UC Berkeley, and UC San Francisco) and at partner organizations in the Bay Area and beyond
- Competitive compensation and benefits commensurate with experience
Benefits
We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world's leading scientists.
The CZ Biohub Network is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.
Pursuant to the California Fair Chance Act, we will consider for employment qualified applicants with arrest and conviction records.
Headhunters and recruitment agencies may not submit resumes/CVs through this website or directly to managers. The CZ Biohub Network does not accept unsolicited headhunter and agency resumes. The CZ Biohub Network will not pay fees to any third-party agency or company that does not have a signed agreement with the CZ Biohub Network.