• Version:

    • 0.4.1
  • Release date:

    • 19 September 2021
  • First released:

    • 26 March 2020
  • Development status:

    • 5 - Production/Stable
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 13
  • Forks: 3
  • Issues + PRs: 9
  • Python versions supported:

    • >=3.8
  • Operating system:

    • OS Independent
  • Requirements:

    • aicsimageio[all] (~=4.1)
    • fsspec[http]
    • napari (>=0.4.11)
    • napari-plugin-engine (>=0.1.4)

napari-aicsimageio

AICSImageIO for napari. Multiple file format reading directly into napari using pure Python.

Features

  • Supports reading metadata and imaging data for:
    • CZI
    • OME-TIFF
    • TIFF
    • Any formats supported by aicsimageio
    • Any additional format supported by imageio

Plugin Variants

screenshot of plugin sorter showing that napari-aicsimageio-in-memory should be placed above napari-aicsimageio-out-of-memory

There are two variants of this plugin that are added during installation:

  • aicsimageio-in-memory, which reads an image fully into memory
  • aicsimageio-out-of-memory, which delays reading ZYX chunks until required.

This allows for incredible large files to be read and displayed.

Examples of Features

General Image Reading

All image file formats supported by aicsimageio will be read and all raw data will be available in the napari viewer.

In addition, when reading an OME-TIFF, you can view all OME metadata directly in the napari viewer thanks to ome-types.

screenshot of an OME-TIFF image view, multi-channel, z-stack, with metadata viewer

Mosaic CZI Reading

When reading CZI images, if the image is a mosaic tiled image, napari-aicsimageio will return the reconstructed image:

screenshot of a reconstructed / restitched mosaic tile CZI

Mosaic LIF Reading

When reading LIF images, if the image is a mosaic tiled image, napari-aicsimageio will return the reconstructed image:

screenshot of a reconstructed / restitched mosaic tile LIF

Citation

If you find aicsimageio (or napari-aicsimageio) useful, please cite as:

AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio

Free software: BSD-3-Clause

  • Version:

    • 0.4.1
  • Release date:

    • 19 September 2021
  • First released:

    • 26 March 2020
  • Development status:

    • 5 - Production/Stable
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 13
  • Forks: 3
  • Issues + PRs: 9
  • Python versions supported:

    • >=3.8
  • Operating system:

    • OS Independent
  • Requirements:

    • aicsimageio[all] (~=4.1)
    • fsspec[http]
    • napari (>=0.4.11)
    • napari-plugin-engine (>=0.1.4)

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