ND2 conversion

Convert ND2 to TIFF or OME-TIFF on Windows and Mac

Convert ND2 files to OME-TIFF, the open TIFF that keeps channel names and pixel size, with the vendor's software, with free Fiji or bfconvert, with a few lines of Python, or in SlideScope without code. Prefer OME-TIFF to a plain TIFF: a plain TIFF usually loses the calibration and channel metadata. And keep unpublished data off online converters, which upload your file.

Download SlideScopeAll conversion options
Lossless OME-TIFFChannels and calibration keptNo upload

Ways to convert ND2 to TIFF

ToolCostPlatformsNotes
Nikon NIS-Elements ViewerFreeWindows (5.22); macOS 1.10, export not documentedFile › Export ND Document (TIF, multipage TIFF, ND2, JPEG2000); Save/Export to TIFF Files with an OME-TIFF option
Fiji / ImageJ with Bio-FormatsFree, open sourceWindows, macOS, LinuxBio-Formats Exporter to OME-TIFF
bfconvert (Bio-Formats tools)Free, open sourceWindows, macOS, LinuxCommand line; batch, BigTIFF, compression
Python (nd2, bioio)Free, open sourceWindows, macOS, Linuxnd2 writes OME-TIFF in one call
SlideScopePaid; export comes with the 3-day free trialWindows 10/11, macOS 14+Lossless OME-TIFF with channels, calibration and stage positions, no code, no upload

Avoid online converters for research data: they upload the file to someone else’s server, and we found none we could recommend for ND2.

Convert ND2 to TIFF in NIS-Elements Viewer (free)

  1. Open the ND2 in NIS-Elements Viewer (free from Nikon).
  2. Choose File › Save/Export to TIFF Files, and pick Standard TIFF or OME-TIFF; tick “Include OME Metadata” to keep the calibration, or “Store into Multipage TIFF” for one file per series.
  3. Or choose File › Export ND Document… to save as TIF, multipage TIFF, ND2 or JPEG2000.

These steps come from Nikon’s Windows user guide (5.21). The Mac viewer (1.10) is an initial release with core features, and Nikon does not document its export options.

Convert ND2 to OME-TIFF in Fiji or with bfconvert (free)

  1. In Fiji, open the ND2 file (it goes through the Bio-Formats importer).
  2. Choose Plugins › Bio-Formats › Bio-Formats Exporter and save as .ome.tif. For files over 4 GB use a BigTIFF extension such as .ome.btf; a plain .tif is limited to 4 GB.

Without opening Fiji, the Bio-Formats command-line tools convert from a terminal (download bftools.zip from the Bio-Formats site):

bfconvert input.nd2 output.ome.tiff
bfconvert -bigtiff -compression LZW -tilex 512 -tiley 512 input.nd2 output.ome.tiff
bfconvert -noflat -pyramid-resolutions 4 -pyramid-scale 2 input.nd2 output.ome.tiff

The output format follows the extension; output is uncompressed unless you pass -compression; -series 0 converts one series only. The pyramid form needs -noflat, which only OME-TIFF supports.

Convert ND2 in Python

The nd2 package reads ND2 and, since version 0.10.0, writes OME-TIFF directly:

import nd2

with nd2.ND2File("input.nd2") as f:
f.write_tiff("output.ome.tif")

For a NumPy array instead, use nd2.imread("input.nd2") or f.asarray(); bioio with its bioio-nd2 plugin also reads ND2.

Convert ND2 to OME-TIFF in SlideScope (no code)

  1. Open the ND2 file in SlideScope on Windows or Mac.
  2. Choose File › Export Current Image as TIFF… and pick a destination. SlideScope writes a lossless OME-TIFF (.ome.tif) with the channel names, colours and pixel size, and never changes the original file.
  3. For many files, choose File › Open Folder, select the files, and run “Export the selected files…” for one OME-TIFF per file, with each stage position kept as its own image inside it; “Extract scenes from the selected files…” writes each stage position as a separate file instead.
  4. Open the result in Fiji, QuPath or any OME-TIFF reader: Fiji hands .ome.tif files to Bio-Formats, which reads the calibration and channels.

Export comes with the 3-day free trial (the free preview opens, measures and annotates up to 5 images). The conversion runs on your own computer; nothing is uploaded.

ND2 conversion questions

Can I convert ND2 to TIFF for free?

Yes. Nikon’s free NIS-Elements Viewer exports ND2 to TIFF and multipage TIFF on Windows, Fiji (free) saves OME-TIFF through the Bio-Formats Exporter, and the free bfconvert and nd2 Python tools convert from a script.

Should I export TIFF or OME-TIFF?

OME-TIFF. It keeps the channel names, the pixel size and the Z, time and position structure; a plain TIFF usually keeps only the pixels, so measurements elsewhere come out in pixels instead of µm.

Why does my exported TIFF look black or very dark?

ND2 images are usually 12- or 16-bit, and a viewer that shows the full 0-65,535 range makes them look dark. The data is fine: adjust brightness and contrast rather than converting to 8-bit, which throws information away.

How do I convert many ND2 files at once?

Loop over the files with bfconvert or the nd2 Python package. In SlideScope, open the folder, select the files and run “Export the selected files…” for one OME-TIFF per file.

Is SlideScope free?

SlideScope is a paid app with a free preview (open, measure and annotate a few of your own images) and a 3-day free trial.

Free preview: open, measure and annotate up to 5 of your own images. No account or card needed. Export, sharing, comparing slides and AI Analysis come with the 3-day free trial: $0 today, then $25/month unless you cancel before it ends. PayPal or card required, and you can cancel anytime from your account. Annual billing is available at $249.99/year, which works out to about two months free.

Convert without uploading

Open your own ND2 files with the free preview, then export lossless OME-TIFF with the 3-day free trial. Already decided? Subscribe now.

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