@hms-dbmi/vizarr v0.3.0
vizarr
Vizarr is a minimal, purely client-side program for viewing Zarr-based images. It is built with
Viv and exposes a Python API using the
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. This means that other valid zarr-python
stores 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 library. We describe a rapid workflow where
comparison of registration methods as well as visual verification of alignnment can be assessed
remotely, leveraging high-performance computational resources for rapid image processing and
Viv for interactive web-based visualization in a laptop computer. The Jupyter Notebook containing
the workflow described in the manuscript can be found in multimodal_registration_vizarr.ipynb.
For more information, please read our preprint doi:10.31219/osf.io/wd2gu.
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
for multiscale and multimodal images. Currently 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 clone this repository and open one of
the example Jupyter Notebooks.
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.
Citation
If you are using Vizarr in your work please cite our preprint:
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." OSF Preprints (2020), doi:10.31219/osf.io/wd2gu