nviz
A tool for creating and visualizing n-dimensional microscopy images.
Science Score: 67.0%
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✓DOI references
Found 4 DOI reference(s) in README -
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Links to: ncbi.nlm.nih.gov, zenodo.org -
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○Scientific vocabulary similarity
Low similarity (16.8%) to scientific vocabulary
Last synced: 6 months ago
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Repository
A tool for creating and visualizing n-dimensional microscopy images.
Basic Info
- Host: GitHub
- Owner: WayScience
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://wayscience.github.io/nViz/
- Size: 7.69 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 3
- Open Issues: 21
- Releases: 4
Created about 1 year ago
· Last pushed 7 months ago
Metadata Files
Readme
Contributing
License
Code of conduct
Citation
README.md
nViz
This project focuses on ingesting a set of TIFF images as OME-Zarr or OME-TIFF. Each input image set1 are organized by channel and z-slices which form four dimensional (4D) microscopy data. These 4D microscopy data contain information for biological objects (such as organoids).
We read the output with Napari, which provides a way to analyze and understand the 3D image data.
1. Image set is loosely defined and changes depending on the context of the data. Here it represents a set of images in multiple dimensions that contain information regarding the same sample. Each image in an imageset is paired data and must be related as such.
Installation
Install nViz from PyPI or from source:
```shell
install from pypi
pip install nviz
install directly from source
pip install git+https://github.com/WayScience/nViz.git ```
Installation notes for Linux
nViz leverages Napari to help render visuals.
Napari leverages PyQT to help build graphical components.
PyQT has specific requirements based on the operating system which sometimes can cause errors within Napari, and as a result, also nViz.
Below are some steps to try if you find that nViz visualizations through Napari are resulting in QT-related errors.
- Attempt to install
python3-pyqt5through your system package manager (e.g.apt install python3-pyqt5). - When using
nVizwithin GitHub Actions Linux environments, consider using pyvista/setup-headless-display-action withqt: truein order to run without general exceptions.
Contributing, Development, and Testing
Please see our contributing documentation for more details on contributions, development, and testing.
Owner
- Name: The Way Lab
- Login: WayScience
- Kind: organization
- Location: United States of America
- Website: https://waysciencelab.com
- Repositories: 17
- Profile: https://github.com/WayScience
The Way Lab at CU Anschutz
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
---
cff-version: 1.2.0
title: nViz
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Dave
family-names: Bunten
orcid: 'https://orcid.org/0000-0001-6041-3665'
- given-names: Michael
family-names: Lippincott
orcid: 'https://orcid.org/0000-0002-8637-1448'
- given-names: Jenna
family-names: Tomkinson
orcid: 'https://orcid.org/0000-0003-2676-5813'
- given-names: Cameron
family-names: Mattson
orcid: 'https://orcid.org/0009-0008-4969-779X'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
repository-code: 'https://github.com/WayScience/nViz'
abstract: >-
A tool for creating and visualizing n-dimensional microscopy images.
keywords:
- python
- microscopy
- profiling
- organoids
- data
- ome-zarr
- napari
- n-dimensional
- way-lab
license: BSD-3-Clause
identifiers:
- description: Software DOI
type: doi
value: "10.5281/zenodo.15800367"
references:
- title: >-
OME-Zarr: a cloud-optimized bioimaging file format with international community support
type: article
database: Bioinformatics
url: http://biorxiv.org/lookup/doi/10.1101/2023.02.17.528834
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date-published: 2023-02-21
identifiers:
- type: doi
value: 10.1101/2023.02.17.528834
- title: Napari
type: software
identifiers:
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value: 10.5281/zenodo.3555620
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repository-code: https://github.com/napari/napari
license: BSD-3-Clause
- title: >-
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
type: article
issn: 1474-760X
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date-published: 2005-05-03
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value: 10.1186/gb-2005-6-5-r47
GitHub Events
Total
- Create event: 13
- Release event: 2
- Issues event: 26
- Delete event: 8
- Member event: 1
- Issue comment event: 25
- Push event: 35
- Pull request review event: 55
- Pull request review comment event: 61
- Pull request event: 50
- Fork event: 3
Last Year
- Create event: 13
- Release event: 2
- Issues event: 26
- Delete event: 8
- Member event: 1
- Issue comment event: 25
- Push event: 35
- Pull request review event: 55
- Pull request review comment event: 61
- Pull request event: 50
- Fork event: 3
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 21
- Total pull requests: 29
- Average time to close issues: about 1 month
- Average time to close pull requests: 9 days
- Total issue authors: 3
- Total pull request authors: 4
- Average comments per issue: 0.05
- Average comments per pull request: 0.66
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 7
Past Year
- Issues: 21
- Pull requests: 29
- Average time to close issues: about 1 month
- Average time to close pull requests: 9 days
- Issue authors: 3
- Pull request authors: 4
- Average comments per issue: 0.05
- Average comments per pull request: 0.66
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 7
Top Authors
Issue Authors
- d33bs (17)
- MikeLippincott (2)
- jenna-tomkinson (1)
Pull Request Authors
- d33bs (20)
- dependabot[bot] (7)
- jenna-tomkinson (1)
- MikeLippincott (1)
Top Labels
Issue Labels
enhancement (10)
bug (2)
Pull Request Labels
dependencies (7)
github_actions (5)
python (2)
Dependencies
.github/workflows/draft-release.yml
actions
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.github/workflows/publish-docs.yml
actions
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.github/workflows/publish-pypi.yml
actions
- actions/checkout v4 composite
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- astral-sh/setup-uv v5 composite
- pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/run-tests.yml
actions
- actions/checkout v4 composite
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- astral-sh/setup-uv v5 composite
- pre-commit/action v3.0.1 composite
pyproject.toml
pypi
- napari [all]>=0.5.5
- napari-ome-zarr >=0.6.1
- numpy <2.1
- ome-zarr >=0.10.2
- tifffile >=2024.12.12
- xmltodict >=0.14.2
- zarr >=2.18.4