napari-rosettasciio 0.0.3

A napari plugin to read and write scientific data formats using RosettaSciIO

napari-rosettasciio

A napari plugin to read and write scientific data formats using RosettaSciIO.

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Overview

This plugin integrates RosettaSciIO with napari, enabling napari to read and write a wide range of scientific data formats, particularly those used in electron microscopy and spectroscopy.

Note: This plugin focuses on scientific data formats not natively supported by napari. Standard image formats (PNG, JPEG, TIFF, BMP, GIF) and NumPy arrays are handled by napari's built-in readers and are excluded from this plugin to avoid conflicts.

Supported File Formats

RosettaSciIO supports many scientific data formats including:

• HDF5-based formats: HyperSpy (.hspy), EMD (.emd), NeXus (.nxs), USID
• Microscopy formats: Digital Micrograph (.dm3, .dm4), MRC (.mrc), FEI/TIA (.ser, .emi)
• Spectroscopy formats: EDAX (.spc, .spd), Bruker (.bcf), Renishaw WiRE (.wdf)
• And many more specialized scientific formats...

For a complete list of supported formats, see the RosettaSciIO documentation.

Installation

You can install napari-rosettasciio via pip:

pip install napari-rosettasciio

Optional Dependencies

To enable support for specific file formats, you can install with optional dependencies:

# For HDF5 formats (HyperSpy, EMD, NeXus, etc.)
pip install "napari-rosettasciio[hdf5]"

# For image formats (PNG, JPEG, etc.)
pip install "napari-rosettasciio[image]"

# For Zarr-based formats
pip install "napari-rosettasciio[zspy]"

# For all formats
pip install "napari-rosettasciio[all]"

Usage

Once installed, the plugin will automatically register with napari. You can then:

1. Open files: Use File > Open or drag and drop files into napari
2. Save files: Use File > Save and select the desired format

The plugin will automatically detect and use the appropriate reader/writer based on the file extension.

Preserving Metadata

The plugin preserves metadata from the original files, including:

• Axes scales and units
• Original metadata structures
• Custom attributes

This metadata is stored in the layer metadata and can be preserved when saving to formats that support it (e.g., HDF5, Zarr).

Format Limitations

Some formats have specific requirements:

• MRCZ (.mrcz): Only supports 3D volumetric data. This format is currently excluded from the writer capabilities as it cannot handle 2D images.

License

Distributed under the terms of the MIT license, "napari-rosettasciio" is free and open source software.

Issues

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

Acknowledgements

This plugin is built on top of RosettaSciIO, which originated from the HyperSpy project. We are grateful to all contributors to these projects.