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  • Welcome
  • Installation
    • Installing Fiji
    • Installing the sciview plugin for Fiji
    • Installing the development version of the sciview plugin for Fiji
  • Demo Gallery & Recipes
    • Published Examples
    • Feature Demos
    • Recipes
  • Basics
    • First Scene
    • Volumetric Data
    • Mesh Processing
  • Image Analysis
    • Creating and Exporting Isosurfaces
    • Image Registration
    • Voxelization
  • Complex Data
    • Point Clouds
    • 3D Segmentations
  • Scripting
    • First scripts
    • Animations
    • Find and Count Cells
  • VR & AR
    • VR & AR
  • Development
    • First Demo Command
    • Customizing the Inspector
    • Update sites
    • Benchmarking
  • Workshops
    • HIP 2021
    • I2K 2020
  • Surveys
    • I2K 2020
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On this page
  • 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

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  1. Workshops

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, 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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