https://github.com/openchemistry/tomviz
Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com, acs.org -
✓Committers with academic emails
20 of 44 committers (45.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
Basic Info
- Host: GitHub
- Owner: OpenChemistry
- License: bsd-3-clause
- Language: C++
- Default Branch: master
- Homepage: https://tomviz.org/
- Size: 22.9 MB
Statistics
- Stars: 339
- Watchers: 34
- Forks: 88
- Open Issues: 137
- Releases: 31
Topics
Metadata Files
README.md
The Tomviz project is developing a cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data. It features a complete pipeline capable processing data from alignment, reconstruction, and segmentation through to displaying, visualizing, and interacting with 3D reconstructions of tomographic data. Many of the data operators are available as editable Python scripts that can be modified in the interface to experiment with different techniques. The pipeline can be saved to disk, and a number of common file formats are supported for importing and exporting data.
The Tomviz project was founded by Marcus D. Hanwell and Utkarsh Ayachit at Kitware, David A. Muller (Cornell University), and Robert Hovden (University of Michigan), funded by DOE Office of Science contract DE-SC0011385.
Installing
We recommend downloading the current stable release, but also provide nightly binaries built by our dashboards for Windows, macOS, and Linux.
Windows: Follow the installation instructions, double-click on the Tomviz icon to launch the application. macOS: After downloading the package double-click to begin installation. Drag the Tomviz icon into your Applications directory – or anywhere else you would like to store it. Double-click on the icon to open it, nightly builds will require right-clicking and selecting open. Linux: A binary (tar.gz) is provided, or it can be built from source. See instructions for building found in the BUILDING.md document.
A Quick Tutorial
- Open a sample dataset by clicking “Sample Menu > Reconstruction ” at the top menubar.
- Create a 3D volumetric visualization by clicking “Visualization > Volume” at the top menubar.
- Interact with your volume in the center panel titled “RenderView”.
User Guide
Start by watching this short video to see Tomviz in action.
Also Tomviz user guide has more detailed information to get started.
Cite Tomviz
When using tomviz in your research, please cite:
Publications using Tomviz
- A Simple Preparation Method for Full-Range Electron Tomography of Nanoparticles and Fine Powders, E. Padgett et al., Microsc. & Microanalys. (2017)
- Physical Confinement Promoting Formation of Cu2O–Au Heterostructures with Au Nanoparticles Entrapped within Crystalline Cu2O Nanorods, E. Asenath-Smith et al., Chem. Mater. (2017)
- Nanomaterial datasets to advance tomography in scanning transmission electron microscopy, B. Levin et al., Nature Scientific Data (2016)
- Graphene kirigami, M.K. Blees et al., Nature (2015)
Contributing
Our project uses GitHub for code review, please fork the project and make a pull request if you would like us to consider your patch for inclusion.
Owner
- Name: Open Chemistry
- Login: OpenChemistry
- Kind: organization
- Location: Global
- Website: https://openchemistry.org/
- Repositories: 57
- Profile: https://github.com/OpenChemistry
Permissively licensed cross-platform tools that provide applications for computational chemistry, materials science, and related areas.
GitHub Events
Total
- Issues event: 2
- Watch event: 17
- Issue comment event: 10
- Fork event: 3
Last Year
- Issues event: 2
- Watch event: 17
- Issue comment event: 10
- Fork event: 3
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Chris Harris | c****s@k****m | 937 |
| Marcus D. Hanwell | m****l@k****m | 603 |
| Patrick Avery | p****y@k****m | 527 |
| Shawn Waldon | s****n@k****m | 483 |
| Cory Quammen | c****n@k****m | 372 |
| Alessandro Genova | a****a@k****m | 241 |
| Yi Jiang | y****5@c****u | 178 |
| Robert Maynard | r****d@k****m | 95 |
| Jonathan Schwartz | j****w@u****u | 78 |
| Utkarsh Ayachit | u****t@k****m | 75 |
| Brianna Major | b****r@k****m | 75 |
| Sebastien Jourdain | s****n@k****m | 49 |
| Alvaro Sanchez | a****z@k****m | 40 |
| Robert Hovden | H****n | 31 |
| Matt McCormick | m****k@k****m | 29 |
| jepietryga | j****a@g****m | 20 |
| T.J. Corona | t****a@k****m | 10 |
| Lijie Tu | L****e@d****u | 9 |
| Elliot Padgett | e****t@g****m | 8 |
| Yi Jiang | y****g@Y****l | 5 |
| Ben Boeckel | b****l@k****m | 5 |
| Dan Allan | d****n@b****v | 4 |
| Yi Jiang | y****g@d****u | 4 |
| Yi Jiang | y****g@d****u | 3 |
| Lijie Tu | L****e@d****u | 3 |
| dependabot[bot] | 4****] | 3 |
| bdalevin | b****7@c****u | 2 |
| Julien Nabet | s****2@y****r | 2 |
| Christian Clauss | c****s@m****m | 2 |
| Yi Jiang | y****g@d****u | 2 |
| and 14 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 39
- Total pull requests: 74
- Average time to close issues: over 1 year
- Average time to close pull requests: about 1 month
- Total issue authors: 18
- Total pull request authors: 9
- Average comments per issue: 2.62
- Average comments per pull request: 0.72
- Merged pull requests: 58
- Bot issues: 0
- Bot pull requests: 5
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 14.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ercius (11)
- cjh1 (7)
- Hovden (4)
- rgmendes13 (2)
- IsaacTieu (1)
- anderskaestner (1)
- Plutonium5793 (1)
- darkworks (1)
- AnkitaMohanty24 (1)
- aaron4444 (1)
- choROPeNt (1)
- RupertPaoZ (1)
- jtschwar (1)
- yurivict (1)
- GeriTopore (1)
Pull Request Authors
- psavery (36)
- jtschwar (11)
- cjh1 (8)
- cryos (7)
- dependabot[bot] (5)
- cclauss (2)
- kevinsmia1939 (2)
- danielballan (2)
- TrellixVulnTeam (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 17
conda-forge.org: tomviz
- Homepage: https://github.com/OpenChemistry/tomviz
- License: BSD-3-Clause
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Latest release: 1.10.0
published over 4 years ago
Rankings
Dependencies
- Pillow ==8.3.2 development
- diskcache ==3.0.1 development
- mock ==2.0.0 development
- pytest ==3.0.6 development
- requests ==2.20.0 development
- diskcache ==3.0.1 development
- h5py ==2.10.0 development
- mock ==2.0.0 development
- pytest ==3.5.0 development
- requests ==2.20.0 development
- click *
- h5py *
- numpy *
- scipy *
- tqdm *
- tomviz/tomviz-dependencies latest build
- library/ubuntu 16.04 build
- library/python 3.7-slim build
- continuumio/miniconda3 latest build