Data

Tools

Indexes

Applications

Experiments

Open Source Science

sciview

sciview is a tool for visualization and interaction with ND image and mesh data

https://github.com/scenerygraphics/sciview

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords

3d fiji hacktoberfest image-processing imagej scenery sciview visualization
Last synced: 6 months ago · JSON representation ·

Repository

sciview is a tool for visualization and interaction with ND image and mesh data

Basic Info
  • Host: GitHub
  • Owner: scenerygraphics
  • License: bsd-2-clause
  • Language: Java
  • Default Branch: main
  • Homepage:
  • Size: 15.3 MB
Statistics
  • Stars: 72
  • Watchers: 9
  • Forks: 20
  • Open Issues: 103
  • Releases: 66
Topics
3d fiji hacktoberfest image-processing imagej scenery sciview visualization
Created over 9 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Build status Image.sc Forum Join the chat

sciview - interactive visualisation in vr for fiji & imagej2

SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It uses scenery as a rendering backend and supports rendering to VR headsets via OpenVR.

sciview running the Game of Life 3D demo

sciview running the Game of Life 3D demo (see Demo > Game of Life 3D).

Documentation is being developed.

Adding to Fiji

Detailed installation instructions can be found in the sciview gitbook.

Should you experience any issues, please try the latest development version, which includes all the latest features and fixes.

Quick Start

Overview of sciview's user interface

Developers

Kyle Harrington, University of Idaho & Ulrik Guenther, MPI-CBG

Contributors

  • Curtis Rueden (University of Wisconsin, Madison)
  • Aryaman Gupta (MPI-CBG)
  • Tobias Pietzsch (MPI-CBG)
  • Robert Haase (MPI-CBG)
  • Jan Eglinger (FMI Basel)
  • Stephan Saalfeld (HHMI Janelia Farm)

Citation

In case you use sciview or scenery in a scientific publication, please cite this paper:

  • Ulrik Günther, Tobias Pietzsch, Aryaman Gupta, Kyle I.S. Harrington, Pavel Tomancak, Stefan Gumhold, and Ivo F. Sbalzarini: scenery — Flexible Virtual Reality Visualisation on the Java VM. IEEE VIS 2019 (accepted, arXiv:1906.06726).

Resources

DevOps

Triggering uploads to the update site:

Add either [SV_IJ_DEPLOY_UNSTABLE] or [SV_IJ_DEPLOY_PRIMARY] to a commit message

Acknowledgements

This software contains the following 3rd party libraries:

  • IntelliJ UI code, by JetBrains (licensed under the Apache Software License 2.0), see src/main/java/com/intellij
  • trove4j, by the Trove4j team (licensed under the Lesser GNU Public License 3.0), see src/main/java/gnu

Owner

  • Name: scenerygraphics
  • Login: scenerygraphics
  • Kind: organization

Citation (CITATION.cff) 

# YAML 1.2
---
abstract: "ImageJ/Fiji is a widely-used tool in the biomedical community for performing everyday image analysis tasks. However, its 3D viewer component (aptly named 3D Viewer) has become dated and is no longer actively maintained. We set out to create an alternative tool that not only brings modern concepts and APIs from computer graphics to ImageJ, but is designed to be robust to long-term, open-source development. To achieve this we divided the visualization logic into two parts: the rendering framework, scenery, and the user-facing application, sciview. In this paper we describe the development process and design decisions made, putting an emphasis on sustainable development, community building, and software engineering best practises. We highlight the motivation for the Java Virtual Machine (JVM) as a target platform for visualisation applications. We conclude by discussing the remaining milestones and strategy for long-term sustainability."
authors: 
  -
    affiliation: "Center for Advanced Systems Understanding, Görlitz, Germany / Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany / Center for Systems Biology, Dresden, Germany"
    family-names: "Günther"
    given-names: Ulrik
    orcid: "https://orcid.org/0000-0002-1179-8228"
  -
    family-names: Harrington
    given-names: "Kyle I.S."
    orcid: "https://orcid.org/0000-0002-7237-1973"
cff-version: "1.1.0"
date-released: 2020-05-04
doi: "10.2312/visgap.20201112"
license: "BSD-2-Clause"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/scenerygraphics/sciview"
title: "Tales from the Trenches: Developing sciview, a new 3D viewer for the ImageJ community"
...

GitHub Events

Total
  • Issues event: 7
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 36
  • Push event: 75
  • Pull request review event: 4
  • Pull request event: 9
  • Fork event: 3
  • Create event: 6
Last Year
  • Issues event: 7
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 36
  • Push event: 75
  • Pull request review event: 4
  • Pull request event: 9
  • Fork event: 3
  • Create event: 6

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 91
  • Total pull requests: 94
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: about 1 month
  • Total issue authors: 17
  • Total pull request authors: 11
  • Average comments per issue: 2.18
  • Average comments per pull request: 0.57
  • Merged pull requests: 70
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 6
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 months
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.2
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kephale (64)
  • smlpt (11)
  • ctrueden (2)
  • rimadoma (2)
  • xulman (2)
  • thuzyp (1)
  • wrongapocalypse (1)
  • odinsbane (1)
  • tpietzsch (1)
  • tferr (1)
  • haesleinhuepf (1)
  • skalarproduktraum (1)
  • yjobic (1)
  • camlloyd (1)
  • elevans (1)
Pull Request Authors
  • kephale (48)
  • skalarproduktraum (15)
  • dependabot[bot] (9)
  • smlpt (8)
  • ctrueden (4)
  • elect86 (3)
  • haesleinhuepf (2)
  • wrongapocalypse (2)
  • camlloyd (1)
  • gitter-badger (1)
  • axtimwalde (1)
  • imagejan (1)
Top Labels
Issue Labels
enhancement (24) longterm (6) needs-verification (6) bug (6) 1.0.0 (2) UX (2) question (1) linux (1) ui (1) confirmed (1) verified (1)
Pull Request Labels
dependencies (10) enhancement (6) bugfix (4) build-system (4) prague-hackathon-2024 (2) bug (1) UX (1)

Dependencies

build.gradle.kts maven
  • graphics.scenery:scenery $sceneryVersion api
  • net.imagej:imagej-mesh 0.8.1 api
  • com.fasterxml.jackson.core:jackson-databind 2.13.1 implementation
  • com.fasterxml.jackson.dataformat:jackson-dataformat-yaml 2.13.1 implementation
  • com.fasterxml.jackson.module:jackson-module-kotlin 2.13.1 implementation
  • com.formdev:flatlaf 1.6.5 implementation
  • io.scif:scifio * implementation
  • io.scif:scifio-bf-compat * implementation
  • net.imagej:ij * implementation
  • net.imagej:imagej-common * implementation
  • net.imagej:imagej-launcher * implementation
  • net.imagej:imagej-legacy * implementation
  • net.imagej:imagej-mesh-io * implementation
  • net.imagej:imagej-ops * implementation
  • net.imagej:imagej-ui-swing * implementation
  • net.imglib2:imglib2 * implementation
  • net.imglib2:imglib2-ij * implementation
  • net.imglib2:imglib2-roi * implementation
  • ome:formats-bsd * implementation
  • ome:formats-gpl * implementation
  • org.jetbrains.kotlin:kotlin-stdlib $ktVersion implementation
  • org.jetbrains.kotlin:kotlin-stdlib-common $ktVersion implementation
  • org.jetbrains.kotlinx:kotlinx-coroutines-core 1.6.0 implementation
  • org.msgpack:jackson-dataformat-msgpack 0.9.0 implementation
  • org.scijava:scijava-common * implementation
  • org.scijava:scijava-search * implementation
  • org.scijava:scijava-ui-awt * implementation
  • org.scijava:scijava-ui-swing * implementation
  • org.scijava:script-editor * implementation
  • org.scijava:scripting-jython * implementation
  • org.scijava:ui-behaviour * implementation
  • sc.fiji:bigdataviewer-core * implementation
  • sc.fiji:bigdataviewer-vistools * implementation
  • sc.fiji:spim_data * implementation
.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • burrunan/gradle-cache-action v1 composite
  • gradle/wrapper-validation-action v1 composite
environment.yml conda
  • git
  • maven
  • openjdk >=8.0.192,<8.1.0a0
  • pip
  • python >=3.8