napari

napari: a fast, interactive, multi-dimensional image viewer for python

https://github.com/napari/napari

Science Score: 77.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
13 of 179 committers (7.3%) from academic institutions
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Keywords

napari numpy python visualization

Keywords from Contributors

closember qt wx tk gtk imaging tensors transcriptomics mesh docs

Last synced: 4 months ago · JSON representation ·

Repository

napari: a fast, interactive, multi-dimensional image viewer for python

Basic Info

Host: GitHub
Owner: napari
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://napari.org
Size: 79.7 MB

Statistics

Stars: 2,453
Watchers: 44
Forks: 450
Open Issues: 1,124
Releases: 0

Topics

napari numpy python visualization

Created over 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing Funding License Citation Codeowners

napari

multi-dimensional image viewer for python

Conda Downloads

napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

We're developing napari in the open! But the project is in an alpha stage, and there will still likely be breaking changes with each release. You can follow progress on this repository, test out new versions as we release them, and contribute ideas and code.

If you want to refer to our documentation, please go to napari.org. If you want to contribute to it, please refer to the contributing section below.

We're working on tutorials, but you can also quickly get started by looking below.

try it out now!

Install uv to try napari. Then launch the program in a terminal window with the command: sh uvx "napari[all]" In the File menu, select Open Sample and select a sample image to get started.

installation

For a full installation, we recommend installing napari into a virtual environment, like this:

sh conda create -y -n napari-env -c conda-forge python=3.11 conda activate napari-env python -m pip install "napari[all]"

If you prefer conda over pip, you can replace the last line with: conda install -c conda-forge napari pyqt

See here for the full installation guide.

simple example

This example uses a data sample from the scikit-image library, but you can pass your own dataset as an array to imshow. From inside an IPython shell, you can open up an interactive viewer by calling

```python from skimage import data import napari

viewer, layers = napari.imshow(data.cells3d(), channel_axis=1, ndisplay=3) ```

napari viewer with a multichannel image of cells displayed as two image layers: nuclei and membrane.

To use napari from inside a script, use napari.run():

```python from skimage import data import napari

viewer, layers = napari.imshow(data.cells3d(), channel_axis=1, ndisplay=3) napari.run() # start the "event loop" and show the viewer ```

features

Check out the scripts in our examples folder to see some of the functionality we're developing!

napari supports six main different layer types, Image, Labels, Points, Vectors, Shapes, and Surface, each corresponding to a different data type, visualization, and interactivity. You can add multiple layers of different types into the viewer and then start working with them, adjusting their properties.

All our layer types support n-dimensional data and the viewer provides the ability to quickly browse and visualize either 2D or 3D slices of the data.

napari also supports bidirectional communication between the viewer and the Python kernel, which is especially useful when launching from jupyter notebooks or when using our built-in console. Using the console allows you to interactively load and save data from the viewer and control all the features of the viewer programmatically.

You can extend napari using custom shortcuts, key bindings, and mouse functions.

tutorials

For more details on how to use napari checkout our tutorials. These are still a work in progress, but we'll be updating them regularly.

mission, values, and roadmap

For more information about our plans for napari you can read our mission and values statement, which includes more details on our vision for supporting a plugin ecosystem around napari. You can see details of the project roadmap here.

contributing

Contributions are encouraged! Please read our contributing guide to get started. Given that we're in an early stage, you may want to reach out on our GitHub Issues before jumping in.

If you want to contribute to or edit our documentation, please go to napari/docs.

Visit our project weather report dashboard to see metrics and how development is progressing.

code of conduct

napari has a Code of Conduct that should be honored by everyone who participates in the napari community.

governance

You can learn more about how the napari project is organized and managed from our governance model, which includes information about, and ways to contact the @napari/steering-council and @napari/core-devs.

citing napari

If you find napari useful please cite this repository using its DOI as follows:

napari contributors (2019). napari: a multi-dimensional image viewer for python. doi:10.5281/zenodo.3555620

Note this DOI will resolve to all versions of napari. To cite a specific version please find the DOI of that version on our zenodo page. The DOI of the latest version is in the badge at the top of this page.

help

We're a community partner on the image.sc forum and all help and support requests should be posted on the forum with the tag napari. We look forward to interacting with you there.

Bug reports should be made on our GitHub issues using the bug report template. If you think something isn't working, don't hesitate to reach out - it is probably us and not you!

institutional and funding partners

Owner

Name: napari
Login: napari
Kind: organization

Repositories: 17
Profile: https://github.com/napari

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: 'napari: a multi-dimensional image viewer for Python'
identifiers:
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  value: 10.5281/zenodo.3555620
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  affiliation: Harvard Medical School
  orcid: https://orcid.org/0000-0002-2409-0181
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- given-names: Grzegorz
  family-names: Bokota
  affiliation: napari; University of Warsaw, Faculty of Mathematics, Informatics, and Mechanics
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  affiliation: Monash eResearch Centre, Monash University
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  affiliation: Iber Lab - ETH Zürich
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repository-code: https://github.com/napari/napari
license: BSD-3-Clause

Committers

Last synced: 7 months ago

All Time

Total Commits: 3,886
Total Committers: 179
Avg Commits per committer: 21.709
Development Distribution Score (DDS): 0.858

Past Year

Commits: 524
Committers: 39
Avg Commits per committer: 13.436
Development Distribution Score (DDS): 0.719

Top Committers

Name	Email	Commits
Grzegorz Bokota	b**b@g**m	551
Talley Lambert	t**t@g**m	477
Nicholas Sofroniew	s**n@g**m	468
Matthias Bussonnier	b**s@g**m	207
Juan Nunez-Iglesias	j**s@m**u	182
Peter Sobolewski	7****D	153
Lorenzo Gaifas	b**g@g**m	132
Kira Evans	c**t@k**e	118
Andy Sweet	a**t@g**m	111
Gonzalo Peña-Castellanos	g**a@g**m	87
pre-commit-ci[bot]	6****]	87
Draga Doncila Pop	1****a	83
Daniel Althviz Moré	1****z	80
Philip Winston	p**n@g**m	69
Kevin Yamauchi	k**i@g**m	68
Lucy Liu	j**6@g**m	60
David Stansby	d**y@g**m	59
alisterburt	a**t@g**m	57
napari-bot	8****t	56
Melissa Weber Mendonça	m**m@g**m	51
Jaime Rodríguez-Guerra	j****p	48
dependabot[bot]	4****]	45
Pam	5****a	43
Genevieve Buckley	3****y	40
Tim Monko	t**o@g**m	35
ziyangczi	4****i	34
Gregory R. Lee	g**7@g**m	24
Carol Willing	c**e@w**m	23
Jordão Bragantini	j**i@c**g	21
Ahmet Can Solak	a**4@k**r	19
and 149 more...

Committer Domains (Top 20 + Academic)

chanzuckerberg.com: 4 monash.edu: 2 pasteur.fr: 2 wisc.edu: 2 dundee.ac.uk: 2 damcb.com: 1 rdil.rocks: 1 tcd.ie: 1 zeroth.me: 1 stowers.org: 1 arlowe.co.uk: 1 amsat.org: 1 mpi-dortmund.mpg.de: 1 ku.edu.tr: 1 czbiohub.org: 1 willingconsulting.com: 1 kne42.me: 1 datajoint.com: 1 mrc-lmb.cam.ac.uk: 1 10xgenomics.com: 1 ucl.ac.uk: 1 virginia.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 1,257
Total pull requests: 2,278
Average time to close issues: about 1 year
Average time to close pull requests: 30 days
Total issue authors: 276
Total pull request authors: 101
Average comments per issue: 4.35
Average comments per pull request: 4.79
Merged pull requests: 1,661
Bot issues: 94
Bot pull requests: 149

Past Year

Issues: 403
Pull requests: 825
Average time to close issues: 12 days
Average time to close pull requests: 7 days
Issue authors: 89
Pull request authors: 44
Average comments per issue: 1.74
Average comments per pull request: 3.97
Merged pull requests: 599
Bot issues: 75
Bot pull requests: 62

View more stats

Top Authors

Issue Authors

psobolewskiPhD (170)
jni (126)
github-actions[bot] (84)
TimMonko (47)
lucyleeow (45)
Czaki (45)
Carreau (40)
sofroniewn (33)
tlambert03 (27)
haesleinhuepf (24)
andy-sweet (23)
GenevieveBuckley (23)
dalthviz (22)
DragaDoncila (21)
alisterburt (19)

Pull Request Authors

Czaki (624)
psobolewskiPhD (247)
dalthviz (120)
Carreau (119)
napari-bot (118)
brisvag (116)
jni (114)
pre-commit-ci[bot] (96)
TimMonko (89)
lucyleeow (74)
dstansby (72)
willingc (54)
dependabot[bot] (52)
DragaDoncila (40)
andy-sweet (31)

Top Labels

Issue Labels

bug (625) feature (228) task (183) UI/UX (52) documentation (48) design (40) priority-high (38) probably solved (35) refactor (22) qt (22) tests (20) priority:high (20) good first issue (19) performance (18) triage:probably solved (16) enhancement (16) vispy (14) contribute:good first issue (13) contribute:sprint (12) maintenance (12) plugins (12) topic:plugins (10) need to reproduce (9) Qt6 (9) priority-low (9) severity-medium (8) topic:vispy (7) api (7) installation (7) question (7)

Pull Request Labels

maintenance (1,117) tests (743) ready to merge (599) qt (579) bugfix (425) enhancement (181) task (128) documentation (108) feature (87) preferences (86) highlight (84) UI/UX (79) typing (52) design (49) performance (41) needs:out-of-draft (32) ui change (28) run-benchmarks (26) dependencies (21) ci (20) example (19) triaged-0.4.18 (17) needs:review (15) bug (15) deprecation (14) api (14) needs:changes (12) breaking change (11) vispy (10) github_actions (9)

Packages

Total packages: 5
Total downloads:
- pypi 107,622 last-month
Total docker downloads: 384

Total dependent packages: 461
(may contain duplicates)
Total dependent repositories: 180
(may contain duplicates)
Total versions: 311
Total maintainers: 6

pypi.org: napari

n-dimensional array viewer in Python

Homepage: https://napari.org
Documentation: https://napari.org
License: BSD 3-Clause
Latest release: 0.6.4
published 4 months ago

Versions: 212
Dependent Packages: 310
Dependent Repositories: 170
Downloads: 107,622 Last month
Docker Downloads: 384

Rankings

Dependent packages count: 0.1%

Dependent repos count: 1.2%

Downloads: 1.5%

Stargazers count: 1.6%

Average: 1.7%

Forks count: 2.7%

Docker downloads count: 3.3%

Maintainers (5)

jni kevin.yamauchi kisharrington ddoncila napari

Last synced: 4 months ago

conda-forge.org: napari

a fast n-dimensional image viewer in Python

Homepage: http://napari.org/
License: BSD-3-Clause AND MIT
Latest release: 0.4.17
published about 3 years ago

Versions: 26
Dependent Packages: 151
Dependent Repositories: 10

Rankings

Dependent packages count: 0.5%

Average: 7.6%

Forks count: 9.0%

Stargazers count: 9.9%

Dependent repos count: 11.1%

Last synced: 4 months ago

proxy.golang.org: github.com/napari/napari

Documentation: https://pkg.go.dev/github.com/napari/napari#section-documentation
License: bsd-3-clause
Latest release: v0.6.4
published 4 months ago

Versions: 69
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 4 months ago

conda-forge.org: napari-menu

provides menu icons for napari

Homepage: http://napari.org/
License: BSD-3-Clause AND MIT
Latest release: 0.4.17
published about 3 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 8.5%

Stargazers count: 9.3%

Average: 25.7%

Dependent repos count: 34.0%

Dependent packages count: 51.2%

Last synced: 4 months ago

pypi.org: test-test-test001001

ada

Documentation: https://test-test-test001001.readthedocs.io/
License: Copyright (c) 2024, All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 10.2%

Average: 33.6%

Dependent repos count: 57.1%

Maintainers (1)

LiuQiang

Last synced: 7 months ago

Dependencies

.github/workflows/resuable_build_wheel.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite

.github/workflows/reusable_coverage_upload.yml actions

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actions/setup-python v4 composite
codecov/codecov-action v3 composite

.github/workflows/reusable_pip_test.yml actions

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aganders3/headless-gui v1 composite
tlambert03/setup-qt-libs v1 composite

.github/workflows/reusable_run_tox_test.yml actions

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binder/environment.yml pypi

jupyter-desktop-server *

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.github/workflows/benchmarks_report.yml actions

actions/github-script v6 composite

.github/workflows/build_docs.yml actions

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actions/upload-artifact v3 composite
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tlambert03/setup-qt-libs v1 composite

.github/workflows/circleci.yml actions

larsoner/circleci-artifacts-redirector-action master composite

.github/workflows/deploy_docs.yml actions

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.github/workflows/docker-singularity-publish.yml actions

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.github/workflows/edit_pr_description.yml actions

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actions/setup-python v2 composite

.github/workflows/label_and_milesone_checker.yml actions

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.github/workflows/labeler.yml actions

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.github/workflows/make_bundle_conda.yml actions

.github/workflows/make_release.yml actions

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.github/workflows/test_comprehensive.yml actions

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styfle/cancel-workflow-action 0.11.0 composite
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.github/workflows/test_prereleases.yml actions

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aganders3/headless-gui v1 composite
tlambert03/setup-qt-libs v1 composite

.github/workflows/test_pull_requests.yml actions

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.github/workflows/test_translations.yml actions

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.github/workflows/test_typing.yml actions

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.github/workflows/test_vendored.yml actions

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peter-evans/create-pull-request v5 composite

.github/workflows/upgrade_test_constraints.yml actions

actions/checkout v3 composite
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.devcontainer/Dockerfile docker

mcr.microsoft.com/vscode/devcontainers/miniconda 0-3 build

napari

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

napari

multi-dimensional image viewer for python

try it out now!

installation

simple example

features

tutorials

mission, values, and roadmap

contributing

code of conduct

governance

citing napari

help

institutional and funding partners

Owner

Citation (CITATION.cff)

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: napari

Rankings

Maintainers (5)

conda-forge.org: napari

Rankings

proxy.golang.org: github.com/napari/napari

Rankings

conda-forge.org: napari-menu

Rankings

pypi.org: test-test-test001001

Rankings

Maintainers (1)

Dependencies