vizarr

A minimal Zarr image viewer based on Viv.

https://github.com/hms-dbmi/vizarr

Science Score: 85.0%

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
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: nature.com
✓
Committers with academic emails
2 of 8 committers (25.0%) from academic institutions
✓
Institutional organization owner
Organization hms-dbmi has institutional domain (dbmi.hms.harvard.edu)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.5%) to scientific vocabulary

Keywords

hidivelab jupyter-notebooks viv zarr

Keywords from Contributors

imaging interactive hubmap ome-tiff openmicroscopy optimizing-compiler mesh interpretability sequences generic

Last synced: 6 months ago · JSON representation ·

Repository

A minimal Zarr image viewer based on Viv.

Basic Info

Host: GitHub
Owner: hms-dbmi
License: mit
Language: TypeScript
Default Branch: main
Homepage: https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr
Size: 37.3 MB

Statistics

Stars: 161
Watchers: 8
Forks: 27
Open Issues: 36
Releases: 0

Topics

hidivelab jupyter-notebooks viv zarr

Created over 5 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Citation

README.md

view multiscale zarr images online and in notebooks

standalone app . python api . open in colab

About

Vizarr is a minimal, purely client-side program for viewing zarr-based images.

⚡ GPU accelerated rendering with Viv
💻 Purely client-side zarr access with zarrita.js
🌎 A standalone web app for viewing entirely in the browser.
🐍 An anywidget Python API for programmatic control in notebooks.
📦 Supports any zarr-python store as a backend.

Multiscale OME-Zarr in Jupyter Notebook with Vizarr

Getting started

Vizarr provides two primary interfaces for interacting with the core viewer:

1. Standalone Web App

You can use the standalone web app by copying and pasting a URL to a Zarr store as the ?source query parameter in the web app.

For example, to view this dataset from the IDR, navigate to the following URL:

https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr

2. Python API

The Python API is an anywidget, allowing programatic control of the viewer in computational notebooks like Jupyter, JupyterLab, Colab, and VS Code. The easiest way to get started is to open a Zarr store and load it into the viewer.

```python import vizarr import zarr

store = zarr.open("./path/to/ome.zarr") viewer = vizarr.Viewer() viewer.add_image(store) viewer ```

To learn more, see the getting started notebook.

Data types

Vizarr supports viewing 2D slices of n-Dimensional Zarr arrays, allowing users to choose a single channel or blended composites of multiple channels during analysis. It has special support for the developing OME-NGFF format for multiscale and multimodal images. Currently, Viv supports int8, int16, int32, uint8, uint16, uint32, float32, float64 arrays, but contributions are welcome to support more np.dtypes!

Limitations

vizarr was built to support the registration use case above where multiple, pyramidal OME-Zarr images are viewed within a Jupyter Notebook. Support for other Zarr arrays is supported but not as well tested. More information regarding the viewing of generic Zarr arrays can be found in the example notebooks.

Citation

If you are using Vizarr in your research, please cite our paper:

Trevor Manz, Ilan Gold, Nathan Heath Patterson, Chuck McCallum, Mark S Keller, Bruce W Herr II, Katy Börner, Jeffrey M Spraggins, Nils Gehlenborg, "Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web." Nature Methods (2022), doi:10.31219/10.1038/s41592-022-01482-7

Owner

Name: Harvard Medical School - Department of Biomedical Informatics
Login: hms-dbmi
Kind: organization
Location: Boston

Website: http://dbmi.hms.harvard.edu/
Repositories: 354
Profile: https://github.com/hms-dbmi

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it using these metadata."
authors:
  - given-names: "Trevor"
    family-names: "Manz"
    affiliation: "Harvard Medical School"
  - given-names: "Will"
    family-names: "Moore"
    affiliation: "Open Microscopy Environment"
title: "Vizarr"
url: "https://github.com/hms-dbmi/vizarr"
preferred-citation:
  type: article
  title: "Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web"
  authors:
    - given-names: "Trevor"
      family-names: "Manz"
      orcid: "https://orcid.org/0000-0001-7694-5164"
      affiliation: "Harvard Medical School"
    - given-names: "Ilan"
      family-names: "Gold"
      orcid: "https://orcid.org/0000-0002-5823-1026"
      affiliation: "Harvard Medical School"
    - given-names: "Nathan Heath"
      family-names: "Patterson"
      affiliation: "Vanderbilt University"
      orcid: "https://orcid.org/0000-0002-0064-1583"
    - given-names: "Chuck"
      family-names: "McCallum"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-4039-9768"
    - given-names: "Mark S."
      family-names: "Keller"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-3003-874X"
    - given-names: "Bruce W."
      family-names: "Herr"
      name-suffix: "II"
      affiliation: "Indiana University"
      orcid: "https://orcid.org/0000-0002-6703-7647"
    - given-names: "Kay"
      family-names: "Börner"
      affiliation: "Indiana University"
      orcid: "https://orcid.org/0000-0002-3321-6137"
    - given-names: "Jeffrey M."
      family-names: "Spraggins"
      affiliation: "Vanderbilt University"
      orcid: "https://orcid.org/0000-0001-9198-5498"
    - given-names: "Nils"
      family-names: "Gehlenborg"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-0327-8297"
  doi: "10.1038/s41592-022-01482-7"
  journal: "Nature Methods"
  month: 5
  year: 2022

GitHub Events

Total

Issues event: 7
Watch event: 35
Delete event: 65
Issue comment event: 108
Push event: 155
Pull request review event: 7
Pull request review comment event: 6
Pull request event: 111
Fork event: 5
Create event: 54

Last Year

Issues event: 7
Watch event: 35
Delete event: 65
Issue comment event: 108
Push event: 155
Pull request review event: 7
Pull request review comment event: 6
Pull request event: 111
Fork event: 5
Create event: 54

Committers

Last synced: about 2 years ago

All Time

Total Commits: 120
Total Committers: 8
Avg Commits per committer: 15.0
Development Distribution Score (DDS): 0.242

Past Year

Commits: 6
Committers: 2
Avg Commits per committer: 3.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Trevor Manz	t**z@g**m	91
Will Moore	w**e@d**k	13
Wei Ouyang	o**7@g**m	6
Nils Gehlenborg	n**s@h**u	3
David Haberthür	e**l@d**h	2
Simon Li	o**l@g**m	2
dependabot[bot]	4****]	2
Norman Rzepka	c**e@n**m	1

Committer Domains (Top 20 + Academic)

normanrz.com: 1 davidhaberthuer.ch: 1 hms.harvard.edu: 1 dundee.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 44
Total pull requests: 174
Average time to close issues: 5 months
Average time to close pull requests: about 1 month
Total issue authors: 22
Total pull request authors: 5
Average comments per issue: 3.18
Average comments per pull request: 1.14
Merged pull requests: 92
Bot issues: 0
Bot pull requests: 66

Past Year

Issues: 6
Pull requests: 68
Average time to close issues: 1 day
Average time to close pull requests: 16 days
Issue authors: 6
Pull request authors: 3
Average comments per issue: 1.17
Average comments per pull request: 0.34
Merged pull requests: 24
Bot issues: 0
Bot pull requests: 44

View more stats

Top Authors

Issue Authors

oeway (11)
will-moore (8)
manzt (5)
aliaksei-chareshneu (2)
jmontoyam (1)
r0f1 (1)
ziw-liu (1)
joshmoore (1)
tischi (1)
edoumazane (1)
d33bs (1)
yarikoptic (1)
claesenm (1)
jcaxle (1)
sbesson (1)

Pull Request Authors

manzt (84)
dependabot[bot] (66)
will-moore (22)
habi (1)
normanrz (1)

Top Labels

Issue Labels

bug (1)

Pull Request Labels

dependencies (66) javascript (58) github_actions (5) enhancement (1)

Dependencies

package-lock.json npm

278 dependencies

package.json npm

@danmarshall/deckgl-typings ^4.3.10 development
@types/node ^14.14.5 development
@types/react-dom ^17.0.0 development
@vitejs/plugin-react ^1.0.1 development
prettier ^2.2.0 development
typescript ^4.5.5 development
vite ^2.5.10 development
@hms-dbmi/viv ^0.12.5
@material-ui/core ^4.11.0
@material-ui/icons ^4.9.1
deck.gl ^8.6.7
imjoy-rpc ^0.2.23
jotai ^1.0.0
p-map ^4.0.0
quick-lru ^6.0.0
react ^17.0.1
react-dom ^17.0.1
reference-spec-reader ^0.1.1
zarr ^0.5.1

example/requirements.txt pypi

fsspec *
imjoy >=0.10.10
imjoy-jupyter-extension >=0.2.14
imjoy-rpc >=0.2.30
ipywidgets >=7.0.0
numba *
numpy *
requests *
scikit-image *
zarr *

.github/workflows/build_and_deploy.yml actions

JamesIves/github-pages-deploy-action 3.7.1 composite
actions/checkout v3 composite
actions/setup-node v3 composite

.github/workflows/test.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite

binder/environment.yml conda

fsspec
ipywidgets
jupyter-server-proxy
numba
numpy
requests
scikit-image
zarr