Free online NDPI to OME.TIFF converter

What the NDPI format is

NDPI is Hamamatsu’s proprietary whole-slide image format. Hamamatsu NanoZoomer scanners create NDPI files when digitizing pathology slides, often alongside associated index or metadata files. You may encounter them in Hamamatsu NDP.view2, NDP.view, QuPath, Fiji, and other applications that use Bio-Formats or OpenSlide readers.

An NDPI file can contain a very large full-resolution image, downsampled viewing levels, multiple image series, and sometimes several focal planes. Its internal metadata and pyramid structure are vendor-specific, so general-purpose TIFF programs may not open it correctly.

What the OME-TIFF format is

OME-TIFF is a TIFF-based format defined by the Open Microscopy Environment. It stores image data in TIFF directories and describes dimensions, channels, pixel sizes, planes, and related information in OME-XML metadata.

For whole-slide images, OME-TIFF can contain tiled, pyramidal resolution levels. That lets compatible viewers display a small overview first and load only the high-resolution tiles required for navigation. The format is supported by Bio-Formats, Fiji, QuPath, napari with suitable plugins, and many microscopy workflows.

OME-TIFF is useful when software needs a documented, interoperable format rather than a scanner-specific file. It does not automatically make an image smaller; output size depends on the source data, tile settings, pyramid levels, and compression.

How to convert NDPI to OME-TIFF

Using Bio-Formats bfconvert

Bio-Formats is the most practical desktop command-line option for preserving microscopy metadata and handling very large images. Install the Bio-Formats package from the Open Microscopy Environment, then run bfconvert from a terminal.

1. Place the NDPI file in a folder with enough free space for the output. A whole-slide OME-TIFF can be several gigabytes.
2. Convert the selected image series with tiled, lossless TIFF output:

bfconvert -overwrite -bigtiff -compression LZW input.ndpi output.ome.tiff

-bigtiff is appropriate for files that may exceed the approximately 4 GB limit of classic TIFF. LZW is lossless; use JPEG only when a smaller file is more important than preserving every source pixel.

If the NDPI contains multiple series, inspect the Bio-Formats series list and convert the required one with a series option such as:

bfconvert -overwrite -series 0 -bigtiff -compression LZW input.ndpi output.ome.tiff

For a pyramidal whole-slide output, use a current Bio-Formats version that supports pyramid writing:

bfconvert -overwrite -bigtiff -compression LZW -pyramid-resolutions 5 -pyramid-scale 2 input.ndpi output.ome.tiff

This creates five resolution levels with a twofold reduction between levels. Adjust the number of levels and scale to the target viewer; very large slides usually benefit from tiled pyramids. Run bfconvert without arguments, or consult the installed version’s help, because available pyramid options vary between Bio-Formats releases.

Using 101convert.com

You can also convert the file on the 101convert.com website for free without installing software. Upload the NDPI, choose OME-TIFF as the output format, start the conversion, and download the result. For clinical or unpublished research slides, check the service’s handling and retention terms before uploading; for large whole-slide files, the desktop method is generally more practical.

Quality, compatibility, and limitations

• Conversion cannot recover detail lost when the scanner stored the source using JPEG compression. Selecting LZW preserves the pixels supplied by the NDPI reader but does not restore discarded information.
• Bio-Formats transfers metadata that it can interpret, including many dimensions and physical pixel sizes, but proprietary scanner fields, annotations, barcode data, and application-specific regions may not map completely to OME-XML.
• Check the output in a whole-slide viewer such as QuPath or Fiji with Bio-Formats. Confirm that the overview, full-resolution view, orientation, pixel dimensions, and physical scale are correct.
• A plain OME-TIFF without a pyramid may open in microscopy software but behave poorly in whole-slide viewers. If navigation is slow or the application reports missing resolution levels, regenerate a tiled pyramidal file.
• Keep the original NDPI as the archival source. The OME-TIFF is an interoperability copy and may omit scanner-specific metadata or additional NDPI series.