Version:

  • 0.1.3

Release date:

  • 17 November 2021

First released:

  • 21 October 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

  • >=3.8

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • imaris-ims-file-reader
  • numpy
  • h5py
  • dask

napari-imaris-loader

Napari plugin for loading Bitplane imaris files '.ims'

This plugin enables viewing of Bitplane Imaris files, including very large datasets. The GIFs below demonstrate rendering of a ~2TB IMS file containing a 2 color whole mouse brain. The plugin has been tested on datasets as large as 20TB.

NOTE: For this plugin to work "File/Preferences/Experimental/Render Images Asynchronously" must be selected.

Open IMS file:

Open IMS file GIF

Render in 3D:

A plugin is provided to dynamically reload the data after selecting the lowest resolution level to be included in the viewer. Since napari only renders the lowest resolution, the user can use this plugin to control the quality of 3D rendering. See features and limitations for tips on suggested usage.

3D Rendering and Quality Adjustment GIF

Features

  • Multiscale Rendering
    • Image pyramids which are present in the native IMS format are automatically added to napari during file loading.
  • Chunks are implemented by dask and matched to the chunk sizes stored in each dataset. (Napari appears to only ask for 2D chunks - unclear how helpful this feature is currently)
  • Successfully handles multi-terabyte multi-timepoint multi-channel datasets.
  • Tested with all sample files provided by Bitplane.
  • Higher 3D rendering quality is enabled by a widget that reloads data after specifying the lowest resolution level (higher number = lower resolution) to be included in the multiscale series.

Known Issues / limitations

  • Currently, this is only an image loader, and there are no features for loading or viewing objects
  • Napari sometimes throws errors indicating that it expected a 3D or 5D array but receives the other.
    • This sometimes but relatively rarely causes napari to crash
    • Would like to enable Asynchronous Tiling of Images, but this results in more instability and causes crashes.
  • Contrast_Limits are currently determined by dtype and not the actual data.
    • float: [0,1], uint8: [0,254], uint16: [0,65534]
    • Future implementations may use the HistogramMax parameter to determine this.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-imaris-loader via pip:

pip install napari-imaris-loader

Change Log:

v0.1.2:

Fixed: Issue where .ims files containing a single color 2D image would not open.

Fixed: Issue where using the widget to change resolutions while in 3D rendering would cause a crash. Now the viewer is automatically forced into 2D rendering mode when the widget is used.

Dependency change: The loader is now dependent in a separate package for loading IMS files. https://pypi.org/project/imaris-ims-file-reader/

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-imaris-loader" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.1.3

Release date:

  • 17 November 2021

First released:

  • 21 October 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

  • >=3.8

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • imaris-ims-file-reader
  • numpy
  • h5py
  • dask

Version:

  • 0.1.3

Release date:

  • 17 November 2021

First released:

  • 21 October 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

  • >=3.8

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • imaris-ims-file-reader
  • numpy
  • h5py
  • dask

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