Skip to content

Commit

Permalink
Add README.md (#12)
Browse files Browse the repository at this point in the history
  • Loading branch information
manzt committed Aug 11, 2020
1 parent 308192d commit 9ab6ef4
Show file tree
Hide file tree
Showing 6 changed files with 46 additions and 14 deletions.
35 changes: 35 additions & 0 deletions README.md
@@ -0,0 +1,35 @@
# vizarr

![Multiscale OME-Zarr in Jupyter Notebook with Vizarr](/screenshot.png)

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.

### 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.

### 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`!

### Getting started
The easiest way to get started with `vizarr` is to open the example [Jupyter Notebook](example/README.md).

### 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.

13 changes: 4 additions & 9 deletions example/README.md
@@ -1,15 +1,10 @@
### Getting started

This example will work in the jupyter notebook (not jupyterlab), and requires the `imjoy-rpc` plugin.

```bash
$ pip install imjoy-rpc
```

```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`.

```bash
$ pip install -U imjoy-jupyter-extension
$ pip install -r requirements.txt
$ jupyter notebook imjoy_example.ipynb
```

7 changes: 7 additions & 0 deletions example/requirements.txt
@@ -0,0 +1,7 @@
numpy
ipywidgets>=7.0.0
scikit-image
imjoy>=0.10.0
fsspec
imjoy-rpc
zarr
Binary file added screenshot.png
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Empty file.
5 changes: 0 additions & 5 deletions src/components/Slider.js

This file was deleted.

0 comments on commit 9ab6ef4

Please sign in to comment.