nd2-rs

Pure Rust library for reading Nikon ND2 microscopy files (v2.0, v2.1, v3.0).

Metadata: attributes(), text_info(), experiment(), sizes(), loop_indices()
Pixel access: read_frame(sequence_index) and read_frame_2d(p, t, c, z)
Encodings: uncompressed and zlib-compressed ImageDataSeq

Installation

[dependencies]
nd2-rs = "0.1.5"

Usage

use nd2_rs::{Nd2File, Result};

fn main() -> Result<()> {
    let mut nd2 = Nd2File::open("image.nd2")?;
    let sizes = nd2.sizes()?;
    let pixels = nd2.read_frame_2d(0, 0, 0, 0)?;
    let frame = nd2.read_frame(12)?; // sequence index
    Ok(())
}

CLI

nd2-rs info image.nd2
nd2-rs frame image.nd2 frame.tif --p 0 --t 0 --c 0 --z 0

info prints concise dataset shape JSON:

{
  "positions": 132,
  "frames": 181,
  "channels": 3,
  "height": 2044,
  "width": 2048
}

frame supports writing a single channel to 16-bit TIFF by sequence or by (p, t, c, z).

Recent fixes improved compatibility with ND2 files that:

store channels in-pixel instead of as separate sequence chunks
use padded uncompressed row strides via uiWidthBytes
expose ImageDataSeq chunk sizes in the file map that do not match the on-disk chunk header
number sequence chunks with position as the outer loop and time as the fast loop

Error reporting

Nd2Error is now grouped by source:

File for malformed/invalid file contents
Input for user-provided indices and arguments
Internal for internal arithmetic/logic issues
Unsupported for unsupported ND2/CLX variants

Docs

DATASTRUCTURE.md – format details and parsing

References

Inspired by the Python nd2 library.

License

MIT OR Apache-2.0

nd2-rs 0.1.5