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, [email protected]
Deborah Schmidt, Max Delbrueck Center for Molecular Medicine, [email protected]
Giuseppe Barbieri, Center for Advanced Systems Understanding (CASUS)
@ HZDR, [email protected]
Justin Buerger, Center for Advanced Systems Understanding (CASUS)
@ HZDR, [email protected]
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, if it is not already installed.
2.Install the sciview update site using these instructions​
Running sciview through Python  (linux only)
1.Install Miniconda, instructions here​
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 - 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. The security certificate on
the CREMI site is currently expired. Here is a temporary link to the
same file.
Developers
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 (Kyle, Deborah, Giuseppe, Justin, 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​

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Contents

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

Pre-workshop instructions

Getting Fiji

Running sciview through Python (linux only)

Getting the data

Developers

Syllabus