I2K 2020

Interactive 3D and virtual reality visualization for scientific images with sciview

Tutors:

• Kyle Harrington, [e-mail]

• Ulrik Günther, [e-mail]

Sessions:

• 2020-11-30 14:00 – 2020-11-30 17:00 UTC

• 2020-12-01 08:00 – 2020-12-01 11:00 UTC

For more details on the 2020 I2K workshop see: https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends/virtual-workshop-program

Pre-workshop instructions

Getting Fiji

1. Follow the Fiji installation instructions, if it is not already installed.

2. Install the sciview update site using these instructions

For Linux64, try our prepackaged Linux64 Fiji here if you have issues

Getting the data

• scripts used in the workshop can be downloaded here - if you don't want to use git, you can just click the green Code button, and click Download ZIP

• data for the 3D segmentation demo can be downloaded here from the CREMI challenge

Developer session

• Please sign up for a Github account if you do not already have one. If you are proficient at git, then this is not necessary

• To follow along with the developer session, we strongly recommend downloading IntelliJ. It will be difficult to provide support for any other development environment during the tutorial session.

Syllabus

• Introductions (Ulrik, Kyle, and everyone attending)

• Getting your sciview and development environment setup

• Overview of the sciview project

• Making your first scene

• Working with volumetric data

• Working with meshes

• Creating sciview scripts

• Making your first sciview demo command

• Custom point clouds

• 3D segmentation data

• Virtual and augmented reality

• Survey