> For the complete documentation index, see [llms.txt](https://docs.scenery.graphics/sciview/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.scenery.graphics/sciview/workshops/hip-2021.md).

# HIP 2021

The summer school is being hosted in gather: <https://gather.town/app/nkxyTbuI84smfiQk/HMC-Workshop-Lounge>

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

Tutors:

* Kyle Harrington, Max Delbrueck Center for Molecular Medicine, <kyle.harrington@mdc-berlin.de>
* Deborah Schmidt, Max Delbrueck Center for Molecular Medicine, <deborah.schmidt@mdc-berlin.de>
* Giuseppe Barbieri, Center for Advanced Systems Understanding (CASUS)

  @ HZDR, <g.barbieri@hzdr.de>
* Justin Buerger, Center for Advanced Systems Understanding (CASUS)

  @ HZDR, <burger@mpi-cbg.de>

Sessions:

* 2021-09-28 13:00      –      2021-09-28 17:00 CEST

For more details here: <https://events.hifis.net/event/148/>

## Pre-workshop instructions

If you use Windows or MacOS, then we suggest following the **Getting Fiji** instructions.

If you use Linux, then we suggest following the **Running sciview through Python** instructions.

### **Getting Fiji**

1. Follow the [Fiji installation instructions](/sciview/installation/installing-fiji.md), if it is not already installed.
2. Install the sciview update site using [these instructions](/sciview/installation/installing-the-development-sciview-plugin-for-fiji.md)

### **Running sciview through Python**  (linux only)

1. Install Miniconda, [instructions here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
2. Download

   <https://www.dropbox.com/s/sjpuqty5w97pg9h/Fiji.app-hip-summer-school-2021.zip?dl=0>
3. Unzip the contents and go to that location in your terminal
4. In your terminal: `conda env create -f sciview-hip.yml`
5. In your terminal: `conda activate sciview-hip`
6. In your terminal: `python launch.py`

### **Getting the data**

* scripts used in the workshop can be downloaded [here](https://github.com/ida-mdc/sciview-hip-2021) - 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). The security certificate on

  the CREMI site is currently expired. Here is a [temporary link](https://www.dropbox.com/s/nwrcz0cai4f7v4m/sample_A_20160501.hdf?dl=0) to the

  same file.

### **Developers**

* 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 (Kyle, Deborah, Giuseppe, Justin, and everyone attending)
* Getting your sciview and development environment setup
* Overview of the sciview project
* Making your [first scene](/sciview/basics/first-scene.md)
* Working with [volumetric data](/sciview/basics/volumetric-data.md)
* Working with [meshes](/sciview/basics/mesh-processing.md)
* Creating [sciview scripts](/sciview/scripting/first-scripts.md)
* Making your [first sciview demo command](/sciview/development/first-demo-command.md)
* [Custom point clouds](/sciview/complex-data/point-clouds.md)
* [3D segmentation data](/sciview/complex-data/segmentations.md)