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# vizarr | ||
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![Multiscale OME-Zarr in Jupyter Notebook with Vizarr](/screenshot.png) | ||
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Vizarr is a minimal, purely client-side program for viewing Zarr-based images. It is built with | ||
[Viv](https://hms-dbmi.github.com/viv) and exposes a Python API using the | ||
[`imjoy-rpc`](https://github.com/imjoy-team/imjoy-rpc), allowing users to programatically view multiplex | ||
and multiscale images from within a Jupyter Notebook. The ImJoy plugin registers a codec for Python | ||
`zarr.Array` and `zarr.Group` objects, enabling Viv to securely request chunks lazily via | ||
[Zarr.js](https://github.com/gzuidhof/zarr.js/). This means that other valid zarr-python | ||
[stores](https://zarr.readthedocs.io/en/stable/api/storage.html) can be viewed remotely with Viv, | ||
enabling flexible workflows when working with large datasets. | ||
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### Remote image registration workflow | ||
We created Vizarr to enhance interactive multimodal image alignment using the | ||
[wsireg](https://github.com/NHPatterson/wsireg) library. We describe a rapid workflow were | ||
comparison of registration methods as well as visual verification of alignnment can be assessed | ||
remotely, leveraging computational resources on remote servers for rapid image processing and | ||
Viv for interactive web-based visualization. For more information, please read our pre-print. | ||
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### 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-Zarr format](https://github.com/ome/omero-ms-zarr/blob/master/spec.md) | ||
for multiscale and multimodal images. Currently [Viv](https://hms-dbmi.github.com/viv) supports | ||
`u1`, `u2`, `u4`, and `f4` arrays, but contributions are welcome to support more `np.dtypes`! | ||
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### Getting started | ||
The easiest way to get started with `vizarr` is to open the example [Jupyter Notebook](example/README.md). | ||
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### 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 thew viewing of generic Zarr arrays can be found in in the example notebooks. | ||
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### Getting started | ||
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This example will work in the jupyter notebook (not jupyterlab), and requires the `imjoy-rpc` plugin. | ||
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```bash | ||
$ pip install imjoy-rpc | ||
``` | ||
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```bash | ||
$ python create_fixture.py # creates ome-zarr test | ||
``` | ||
This example will work in the jupyter notebook (not jupyterlab), and requires the `imjoy-jupyter-extension`. | ||
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```bash | ||
$ pip install -U imjoy-jupyter-extension | ||
$ pip install -r requirements.txt | ||
$ jupyter notebook imjoy_example.ipynb | ||
``` | ||
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numpy | ||
ipywidgets>=7.0.0 | ||
scikit-image | ||
imjoy>=0.10.0 | ||
fsspec | ||
imjoy-rpc | ||
zarr |
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