Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
manzt authored Jul 19, 2024
1 parent 360a561 commit 08d33a3
Showing 1 changed file with 19 additions and 18 deletions.
37 changes: 19 additions & 18 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,17 +7,14 @@
<span>view multiscale zarr images online and in notebooks</span>
<br>
<br>
<a href="https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr">app</a> .
<a href="./python/notebooks/getting_started.ipynb">getting started</a>
<a href="https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr">standalone app</a> .
<a href="./python/notebooks/getting_started.ipynb">python api</a> .
<a href="https://colab.research.google.com/github/hms-dbmi/vizarr/blob/main/python/notebooks/mandelbrot.ipynb">open in colab</a>
</p>
</samp>
</p>

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/hms-dbmi/vizarr/blob/main/python/notebooks/mandelbrot.ipynb)

<center>
<img src="./assets/screenshot.png" alt="Multiscale OME-Zarr in Jupyter Notebook with Vizarr" width="400">
</center>
## About

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

Expand All @@ -29,16 +26,11 @@
- 📦 Supports any `zarr-python` [store](https://zarr.readthedocs.io/en/stable/api/storage.html)
as a backend.

### 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!
<p align="center">
<img src="./assets/screenshot.png" alt="Multiscale OME-Zarr in Jupyter Notebook with Vizarr" width="500">
</p>

### Getting started
## Getting started

Copy and paste a URL to a Zarr store as the `?source` query parameter in the
**[web app](https://hms-dbmi.github.io/vizarr/)**. For example, to view the
Expand Down Expand Up @@ -66,13 +58,22 @@ viewer.add_image(store)
viewer
```

### Limitations
## 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
## Citation

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

Expand Down

0 comments on commit 08d33a3

Please sign in to comment.