Bioimage Scientist - Image Processing for Light-sheet Microscopy

Dear Colleagues,

Very excited to announce here that my team at the CZ Biohub is hiring a ‘Bioimage Scientist’ for image processing (and analysis) of 5D light-sheet microscopy data and beyond. The ideal candidate will be familiar with concepts in optics and 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 within the scientific Python ecosystem.

Apply here:

Relevant tweet:

More details:

The Chan Zuckerberg Biohub ("CZ Biohub”) is an independent nonprofit medical research organization based in the San Francisco Bay Area. The Chan Zuckerberg Biohub supports scientific research to cure, prevent or manage disease in our children’s lifetime. Our mission is to understand the fundamental mechanisms underlying disease and to develop new technologies that will lead to actionable diagnostics and effective therapies. We harness the power and possibility of collaboration to drive discovery and set the standard for open, impactful science. For more information, please visit czbiohub.org.

As part of a new intramural collaborative effort that spans our Cell Atlas, Infectious Disease, and Technology Initiatives, the CZ Biohub has several projects that involve large-scale 5D light-sheet imaging over a wide range of scales: from cells to whole organisms. In this context, the CZ Biohub is investing resources and talent in image processing.

Opportunity

We are currently seeking an outstanding Bioimage Scientist to help develop a software suite for large-scale light-sheet image storage, processing and visualization that will leverage all latest technologies and libraries such as napari , Cupy , Dask , Zarr , scikit-image , PyTorch , and more. The individual will be embedded in the team led by Loic A Royer – a cofounder of the napari project. The main responsibilities will be developing open source software for state-of-the-art image processing of 5D microscopy data. The individual will have the opportunity to closely collaborate with scientists and engineers within CZ Biohub developing state-of-the-art multi-color, multi-modal, and volumetric imaging instruments. Moreover, the candidate is expected to foster existing ties to upstream projects such as: napari , zarr , dask , scikit-image, as well as with our local community of collaborators at UCSF, Berkeley, Stanford and beyond. Overall, this is an exciting chance to be embedded in a highly collaborative and well-funded scientific environment, with great opportunities for networking and skill development.

Recent PhD graduates in Microscopy, Optics, Physics, or Electronic Engineering or Computer science, or related topics with a passion for open-source development, image processing, and image analysis are highly encouraged to apply. The ideal candidate will be familiar with concepts in optics and 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.

Responsibilities

  • Development of image processing algorithms for large-scale 5D imaging
  • Open Source community building

Requirements

  • 4+ years of experience in software development in Python, and familiarity with professional software development concepts and tools. A successful candidate must have experience with open source software development, and have worked with large code-bases and complex applications, not just scripts.
  • PhD in Optics, (Computational) Microscopy, Computer Science, EECS, ML/AI/DL or related discipline. PhD level can be waived if the candidate demonstrates exceptional knowledge and experience
  • 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

Desired Experience

  • Experience writing code for GPUs (OpenCL, CUDA)
  • Experience handling multi-terabyte sized datasets
  • Experience with fluorescence imaging
8 Likes

Sounds amazing! Really glad there are positions like these, and hope some are still available once I get out and about :slight_smile: