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OpenReadout

napari

The napari-openreadout plugin opens microscopy files in napari without converting them first.

Terminal window
pip install napari napari-openreadout
napari slide.svs

You can also use File › Open in napari, or viewer.open(path, plugin="napari-openreadout") from Python.

The plugin registers for the image formats OpenReadout reads, including CZI, ND2, LIF, Olympus OIR, OIB, OIF and VSI, whole-slide SVS, NDPI and QPTIFF, Imaris, OME-TIFF, OME-Zarr, MetaMorph, Hamamatsu DCIMG and the electron-microscopy formats MRC, DM3/DM4, SER and EMD.

What you get:

  • Each image in the file (a CZI scene, an ND2 position, a LIF series) is its own layer.
  • Each channel is a separate layer, named and coloured as in the file. RGB images stay one layer.
  • Layers are scaled by the pixel size in micrometres (and the time step in seconds), so 3D views and the scale bar are correct.
  • Layers are lazy dask arrays. napari decodes a plane, or for large tiled planes the tiles in view, only when it displays it.
  • Files that store a pyramid, such as whole-slide images, open as multiscale layers.

Without napari, napari_openreadout.read(path) returns the same layer data.

If another installed plugin also claims an extension, napari asks which reader to use, or you can pass plugin="napari-openreadout".

From Python, without the plugin

The Python package gives you the same lazy arrays, if you want to build the layers yourself:

import napari
import openreadout


f = openreadout.File("run.czi")             # keep it open while the viewer is up
im = f.images[0]
ps = im.get("physical_size", {})
viewer = napari.Viewer()
viewer.add_image(
    f.to_dask(0),                           # (T, C, Z, Y, X)
    channel_axis=1,
    name=[ch.get("name", f"c{ch['index']}") for ch in im.get("channels", [])] or None,
    scale=(1, ps.get("z", 1), ps.get("y", 1), ps.get("x", 1)),
)
napari.run()

For a pyramid, pass f.pyramid(0) with multiscale=True instead.

From an export

An OME-TIFF or OME-Zarr export opens with napari’s own readers or with plugins such as napari-ome-zarr. Use this when you want a file to hand to someone else:

Terminal window
openreadout export run.czi -o run.ome.tiff