Intern, Advanced Bioimaging

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
  Responsibilities

Responsibilities: 

• 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

Preferred

• 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