Intern, Advanced Bioimaging

Denali Therapeutics

Denali Therapeutics

South San Francisco, CA, USA
Posted on Saturday, November 18, 2023

Denali Therapeutics is dedicated to developing breakthrough therapies for patients with neurodegenerative diseases through deep commitment to understanding degeneration biology and rigorously applying the principles of translational medicine. We are excited to offer an internship with the Advanced Bioimaging team at Denali Therapeutics, an interdisciplinary group working at the interface of biology, informatics, and computer science.

The Opportunity

The Advanced Bioimaging team is seeking to recruit an intern to help characterize biodistribution of investigative therapies in animal models of neurodegenerative disease using tissue clearing and light sheet microscopy. They will work in close collaboration with colleagues in Discovery Biology, Preclinical Translational Science, and Biometrics to execute this project. The successful candidate will gain an in-depth understanding of modern microscopy and image analysis techniques and work in a fast-moving industry environment with guidance from an experienced mentor in the field of bioimaging.

Potential projects include one or more of the following:

  • Design and implement an image processing pipeline to segment and classify cell types and assign them to brain regions in 3D light sheet images
  • Design and implement a computational pipeline to segment and characterize extended brain structures such as blood vessels, white matter tracts, or ventricles in 3D light sheet images
  • Develop and characterize methods to scale analyses to multi-terabyte datasets using approaches such as GPU acceleration, high performance computing, or cloud computing


  • Write reproducible analysis pipelines, contribute to code review, and document, test and deploy code
  • Collaborate with Discovery Biology and biomarker scientists to develop features and metrics to quantify drug delivery to regions and cell types of interest
  • Make detailed observations, analyze data, interpret results, and communicate clearly
  • Present results onsite at cross-functional and departmental meetings as well as at final intern poster session

Position Requirements

  • Currently pursuing a BS, MS, or PhD in Computer Science, Data Science, Bioinformatics, Computational Biology, or related fields
  • Experience with Python, machine learning frameworks such as scikit-learn, tensorflow, or pytorch, and command line and shell scripting
  • Strong organizational and communication skills with the ability to work both independently and in a team environment
  • Experience presenting data analysis methods and results to a small team
  • Creative and inquisitive thinker who is eager to explore and learn new skills


  • Experience with image processing and analysis techniques (e.g. signal processing, machine learning, clustering and feature extraction, high dimensional dataset analysis
  • Experience with parallelization/acceleration libraries such as dask, numba, pycuda, or pyopencl and data pipeline frameworks such as joblib, snakemake, or knime

Denali is committed to its core company value of unity by creating a diverse and inclusive environment. We are proud to be an equal opportunity employer and do not discriminate against any employee or applicant for employment because of race, color, sex, age, national origin, religion, sexual orientation, gender identity and/or expression, status as a veteran, basis of disability, or any other federal, state, or local protected class.

The expected wage for this position based on the South San Francisco California office location is $20.96 per hour for BA/BS, $25.87 per hour for MS and $31.82 per hour for PhD. Paid holiday time off is based on Denali's designated holidays. Interns who live more than 50 miles away from the office are eligible for an additional housing stipend.

*This compensation and benefits information is based on Denali’s good faith estimate as of the date of publication and may be modified in the future.

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Job Facts

  • Start Date: Summer 2024
  • Length of Assignment: 10 - 12 weeks
  • Location: South San Francisco, CA
  • Job Type: Paid Internship