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TOOLS.md

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Useful ND2 and OME TIFF tools

ND2 SDK

Nikon's official ND2SDK.

NIS-Elements Viewer

The NIS-Elements Viewer is a baseline ND2 file viewer. It can serve as a reference for visual inspection of ND2 test files.

ND2 to OME-TIFF Converter

An ND2 to OME-TIFF Converter application can be downloaded from the Nikon ND2SDK website. The current version (NIS_ND2ToOMETIFFConverter_Setup_5.40.00_1611.exe) does not create pyramidal OME TIFF files however.

Bioformats

The Bioformats command line tools (bfconvert, showinf, tiffcomment) are useful for inspecting OME TIFF file structure and metadata, and as a baseline for converting ND2 files to OME TIFF using an alternative (Java-based) library.

Here are a few typical use cases:

Converting ND2 to tiled pyramidal OME TIFF with bfconvert

set BF_MAX_MEM=4g
bfconvert.bat -no-upgrade -bigtiff -pyramid-scale 2 -pyramid-resolutions 6 -noflat -tilex 256 -tiley 256 input_image.nd2 pyramidal.ome.tif

Inspecting the structure of an OME TIFF file

showinf.bat pyramidal.ome.tif

Inspecting the OME XML atrributes in an OME TIFF file

tiffcomment.bat pyramidal.ome.tif