# I2K 2020

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

Tutors:

* Kyle Harrington, <kyle.harrington@mdc-berlin.de>
* Ulrik Günther, <ulrik.guenther@hzdr.de>

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](https://docs.scenery.graphics/sciview/installation/installing-fiji), if it is not already installed.
2. Install the sciview update site using [these instructions](https://docs.scenery.graphics/sciview/installation/installing-the-development-sciview-plugin-for-fiji)

For Linux64, try our prepackaged Linux64 Fiji [here](https://www.dropbox.com/s/yjorzgsl39u03g2/Fiji.app-sciview-i2k.zip?dl=0) if you have issues

**Getting the data**

* scripts used in the workshop can be downloaded [here](https://github.com/kephale/sciview-i2k/tree/main/scripts) - 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](https://cremi.org/static/data/sample_A_20160501.hdf) from the [CREMI challenge](https://cremi.org)

**Developer session**

* Please [sign up for a Github account](https://github.com/join) 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](https://www.jetbrains.com/idea/download/). 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](https://docs.scenery.graphics/sciview/basics/first-scene)
* Working with [volumetric data](https://docs.scenery.graphics/sciview/basics/volumetric-data)
* Working with [meshes](https://github.com/scenerygraphics/sciview-docs/tree/a59da827beb64c1e6ce37da3ce44bdc61943fb81/image-analysis/mesh-processing.md)
* Creating [sciview scripts](https://docs.scenery.graphics/sciview/scripting/first-scripts)
* Making your [first sciview demo command](https://docs.scenery.graphics/sciview/development/first-demo-command)
* [Custom point clouds](https://docs.scenery.graphics/sciview/complex-data/point-clouds)
* [3D segmentation data](https://docs.scenery.graphics/sciview/complex-data/segmentations)
* [Virtual and augmented reality](https://github.com/scenerygraphics/sciview-docs/tree/a59da827beb64c1e6ce37da3ce44bdc61943fb81/XR/VR-AR.md)
* [Survey](https://docs.scenery.graphics/sciview/surveys/i2k-2020)