Program

Introduction, goals, and schedule

LifeCanvas - Clearing techniques and sample preparation (confirm with the LifeCanvas team)

Miltenyi - Data acquisition. Demonstration of best practices for image acquisition using example datasets (confirm with the Miltenyi team)

This tutorial will give an introduction to the SPIMquant workflow, and demo data will be provided to attendees to follow-along on their laptops. Links: Intro slides: https://www.khanlab.ca/SPIMquant-intro/ Analysis notebook: https://colab.research.google.com/drive/1JsSBtBV1IwNu5D0dm2N3zLNwMW7tcPnp?usp=sharing Example OME-Zarr from Digital Alliance Cloud: https://ome.github.io/ome-ngff-validator/?source=https://object-arbutus.alliancecan.ca/a8337d65c739485795cd19794e1fffa6:mind-public/workshop-data/AS319.ome.zarr Prerequisites: Create a Google Colab account (google account), Optionally: Install ITKsnap on your system (www.itksnap.org)

Prior to the session, please ensure that you have downloaded the free version of Imaris. https://imaris.oxinst.com/imaris-viewer#