scallops.io.read_image

scallops.io.read_image(path, dask=False, scene_id=None, tmp_dir=None, **kwargs)

Read a single image from various supported formats. This function reads image data from a single file or zarr group. It supports various file formats including tiff, nd2, and other Bio- Formats supported formats. The returned data is represented as a xarray DataArray with dimensions (t, c, z, y, x).

To read a directory of images, see: read_experiment().

Parameters:

  • path (str | Path | Group) – Path to the image file or zarr group.

  • dask (bool) – Whether the returned DataArray should be a dask or numpy array.

  • scene_id (None | str | int) – A valid scene id or index to read a specific scene from the image.

  • tmp_dir (str | None) – Temporary directory to save non-local nd2 files (default is None).

  • kwargs – Additional arguments to pass to the bioio.BioImage constructor.

Returns:

DataArray with the dimensions (t, c, z, y, x).

Example:

Return type:

DataArray

import scallops.io

# Read an image
image_path = "path/to/your/image.tiff"
image = scallops.io.read_image(image_path)

# Optionally, specify a scene id
scene_id = 0
image_with_scene = scallops.io.read_image(image_path, scene_id=scene_id)