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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

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Last updated 3 years ago

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The summer school is being hosted in gather:

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:

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

Running sciview through Python (linux only)

  1. Download

  2. Unzip the contents and go to that location in your terminal

  3. In your terminal: conda env create -f sciview-hip.yml

  4. In your terminal: conda activate sciview-hip

  5. In your terminal: python launch.py

Getting the data

  • data for the 3D segmentation demo can be downloaded

    same file.

Developers

Syllabus

  • Introductions (Kyle, Deborah, Giuseppe, Justin, and everyone attending)

  • Getting your sciview and development environment setup

  • Overview of the sciview project

Follow the , if it is not already installed.

Install the sciview update site using

Install Miniconda,

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

from the

. The security certificate on

the CREMI site is currently expired. Here is a to the

Please 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 . It will be difficult to provide support for any other development environment during the tutorial session.

Making your

Working with

Working with

Creating

Making your

https://gather.town/app/nkxyTbuI84smfiQk/HMC-Workshop-Lounge
https://events.hifis.net/event/148/
Fiji installation instructions
these instructions
instructions here
https://www.dropbox.com/s/sjpuqty5w97pg9h/Fiji.app-hip-summer-school-2021.zip?dl=0
here
here
CREMI challenge
temporary link
sign up for a Github account
downloading IntelliJ
first scene
volumetric data
meshes
sciview scripts
first sciview demo command
Custom point clouds
3D segmentation data