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Fractal ND2 Converters

Fractal ND2 Converters is a collection of Fractal tasks that convert Nikon ND2 microscopy files into OME-Zarr format.

Supported Tasks

Task Output Description
Convert Nikon ND2 Image to OME-Zarr OME-Zarr Image(s) Converts a single .nd2 file, or a folder of .nd2 files, into one or more standalone OME-Zarr images
Convert Nikon ND2 Plate to OME-Zarr OME-Zarr HCS Plate Converts a folder of .nd2 files belonging to a multi-well plate acquisition into an OME-Zarr HCS plate

Each converter reads the native Nikon metadata embedded in the ND2 file(s) and produces a well-structured OME-Zarr dataset that can be viewed in tools like napari or processed with downstream Fractal tasks.

Installation

pip install fractal-nd2-converters

How It Works

Each converter is implemented as a Fractal Compound Task that consists of two steps:

  1. Init task — Parses the ND2 metadata, creates the OME-Zarr structure, and generates a parallelization list.
  2. Compute task — Reads the raw image tiles and writes them into the OME-Zarr dataset. This task runs in parallel across wells or images.

You configure the init task with one or more acquisitions (paths to your .nd2 files or folders) and the converter handles the rest.

Condition Tables

You can attach experimental metadata (drug treatments, concentrations, replicates, etc.) to wells using a condition table CSV file. See the Condition Tables guide for details.

Part of the Fractal OME-Zarr converters ecosystem

This converter is a thin, format-specific layer built on ome-zarr-converters-tools, the shared engine that handles tiling, image registration, and OME-Zarr writing for the whole Fractal converter family. Because they all share that engine, every converter offers the same options, behavior, and development workflow.

Sibling converters built on the same tooling: