CytoData Symposium 2022: Workshops

Amazon Web Services: Machine learning using Kubeflow

This will be a beginner-level workshop that introduces you to Kubeflow, an open-source machine learning toolkit for Kubernetes. It will go over basic concepts of Kubernetes, Kubeflow components, and include a demo of ML using Kubeflow running on Amazon Elastic Kubernetes Service (Amazon EKS). 

Agenda: 

  • Kubernetes concepts 
  • Introduction to Kubeflow 
  • ML using Kubeflow 

Materials to bring: 

  • Personal laptop 

Chan Zuckerberg Initiative: napari: a multidimensional image viewer and analysis platform for Python

napari is an open-source, community-built, python-based image viewer that provides fast, interactive visualization and analysis of multi-dimensional data.  At its core, it provides critical viewer features out-of-the-box, such as support for large multi-dimensional data; provided “layers” to simultaneously visualize images, models, and analysis results; and easy manual, interactive annotation in 3D. To expand napari’s capabilities, the napari-hub is a platform to discover, install, and share napari plugins that tackle various domain-specific visualization and analysis needs. In addition, as a python-based tool, napari is compatible with Jupyter Notebooks for custom workflows and batch processing. 

In this 2-hour workshop, you’ll learn about napari’s capabilities and get firsthand experience using napari with plugins from the napari-hub to visualize multi-dimensional datasets, complete classical and ML-based segmentation workflows, and profile cells based on segmented features. 

Materials to bring: 

  • Personal Laptop 
  • Your own data (optional) 
  • Downloaded and installed napari 

Allen Institute for Cell Science: Open-source tools and resources for image data analysis

Agave Tutorial

We will use this workshop to showcase three different tools and topics developed and/or used here at the Allen Institute for Cell Science: Simularium Viewer, Agave, and 3D shape analysis. 

The Simularium Viewer makes it easy to share and interrogate interactive 3D visualizations of biological simulation trajectories and related plots directly in a web browser. Its primary goal is to facilitate collaborations among experimental and computational biologists by removing major challenges to sharing, accessing, and comparing simulation results. In this workshop we will demo the current viewer, and review how you can load your own data and generate links for sharing or to include in publications. We will also discuss our plans for new features, including viewing model outputs live as they calculate in the cloud. 

Materials to bring: Personal laptop (optional) 

Agave is a visualization tool for multichannel volume data.  It uses cinematic rendering methods to generate high quality images with lighting and shadows.  The workshop will be a guided tour of the features of Agave.  We will walk through a typical session, from loading the data to refining its appearance. 

Materials to bring: 

Quantification of cell shape and its relation with cell function is a central question in cell biology. Our workshop will discuss shape parameterization and introduce 3D shape analysis using spherical harmonics. To do so, we will use data and tools developed in our paper "Integrated intracellular organization and its variations in human iPS cells 

Materials to bring: 

  • Personal laptop 
  • Github account information 

Zeiss: Create deep learning models and data- and Image processing workflows using the Apeer platform and python packages created by Zeiss

The workshop will be focused on various tools and python packages published by ZEISS for reading CZI images, exchanging Deep-Learning models and general image processing. The following topics will be covered: 

  • Training a Deep-Learning Model in APEER and use it in your python code or inside Napari 
  • Reading, processing and writing CZIs using pylibCZIrw 
  • Creating an APEER module from your own python code 

Materials to bring: 

  • Laptop (Windows or Linux) with python environment. (For MAC users we might need to switch to Colab notebooks for some parts) 
  • Basic knowledge in using Git 
  • Valid APEER account (please register at www.apeer.com