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ND2 Image

Converts a Nikon .nd2 file, or a folder of .nd2 files, into one or more standalone OME-Zarr images (not a plate structure).

Expected File Structure

Input Output
A single .nd2 file One OME-Zarr image
A folder of .nd2 files One OME-Zarr image per file 
Acquisition.nd2 → OME-Zarr image

or

{folder}/
├── {filename1}.nd2 → OME-Zarr image 1
├── {filename2}.nd2 → OME-Zarr image 2
└── ...

If a .nd2 file contains multiple stage positions (the ND2 P dimension), each position becomes a positioned field of view inside that image. The fields of view are placed according to their stage positions and assembled into a single image by ome-zarr-converters-tools (see Tiling Mode).

Note

For plate acquisitions where filenames contain Well (e.g. WellA01{filename}.nd2), use the ND2 Plate task instead. If positions were split into separate files (e.g. via the "Split Multipoints" option), each file is converted into its own OME-Zarr image.

Metadata

The converter extracts the following from the ND2 file:

  • Stage positions (X, Y) for each field of view
  • Channel names, emission wavelengths, and colors
  • Pixel size (XY and Z spacing in micrometers)
  • Time spacing (for time-series acquisitions)
  • Image shape (X, Y, Z, C, T)

Task Parameters

Field Type Default Description
Path str required Path to a .nd2 file, or a folder containing .nd2 files.
Zarr Name str or null null Custom name for the output OME-Zarr image(s). Defaults to the file or folder name. For folders, the sanitized file stem is appended to form each image's name.
Advanced AcquisitionOptions {} Advanced options: channel/pixel-size overrides, stage corrections, and filters. See Converters Overview.

Limitations

  • This task has been tested on a limited set of acquisitions (see this Zenodo record). It may not work on all Nikon .nd2 acquisitions.
  • For files with multiple stage positions (the P dimension), the file metadata must contain an XYPosLoop entry, otherwise conversion fails.

Python API

The converter is also available as a regular Python function, for use outside Fractal:

from fractal_nd2_converters import ND2ImageAcquisitionModel, convert_nd2_single_image

convert_nd2_single_image(
    zarr_dir="/path/to/zarr_dir",
    acquisitions=[
        ND2ImageAcquisitionModel(path="/path/to/Acquisition.nd2"),
    ],
)

See How to Run the Converters for the full list of parameters and more examples.