Jupyter, Microscopy, and On-demand Dask Cloud Clusters

Christiana Cromer May 3, 2021

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Matt McCormick, who works at Kitware maintaining the Insight Toolkit (ITK) library, joins Hugo Bowne-Anderson to discuss large-scale microscopic image visualization and analysis with on-demand Dask cloud clusters.

Web-based methods are well-suited to solve scientific microscopy challenges such as large images, remote datasets, and reproducibility.

We’ll discuss how to apply the PyData stack (dask, jupyter, itk, scikit-image, xarray, zarr, and itkwidgets) inside interactive Jupyter notebooks to gain insights from 2D and 3D microscopy datasets. We will discuss web-based image visualization, image data storage for the web, and distributed image processing in the cloud.

After attending, you’ll know:

  • How to create a consistent software environment to use Jupyter with Coiled Dask clusters
  • How to interactively explore your 3D microscopy volumes in Jupyter with itkwidgets
  • How to store your images for distributed processing with Dask and the PyData stack

Join us Thursday, May 27th at 5 pm US Eastern time by signing up below and dive into the wonderful world of large-scale microscopic image visualization and analysis with Dask!