ndpi2tiff

NAME

  ndpi2tiff - Convert a NDPI (digital pathology) file into TIFF

USAGE

  ndpi2tiff [options] file.ndpi

DESCRIPTION

ndpi2tiff opens file.ndpi and converts it into a standard TIFF file. The information about the magnification and z-offset of each image is stored in a TIFF ``image description'' field.

The name of the output file is derived from the name of the input file, removing the .ndpi suffix (if any) and adding the .tif suffix.

OPTIONS

-m

Put in output file only the microscopic images contained in the input NDPI file (thus ignore the macroscopic image(s) or map(s)).

-8

Force output file to use the BigTIFF extension to the TIFF specification (supported by LibTIFF as of version 4.0). This option is needed if the output file is larger than 4 GiB.

-B

Force output to be written with Big-Endian byte order. This option only has an effect when the output file is created or overwritten and not when it is appended to.

-C

Suppress the use of ``strip chopping'' when reading images that have a single strip/tile of uncompressed data.

-c

Specify the compression to use for data written to the output file: none for no compression, packbits for PackBits compression, lzw for Lempel-Ziv & Welch compression, zip for Deflate compression, lzma for LZMA2 compression, jpeg for baseline JPEG compression, g3 for CCITT Group 3 (T.4) compression, and g4 for CCITT Group 4 (T.6) compression. By default ndpi2tiff will compress data according to the value of the Compression tag found in the source file, that is, JPEG.

The CCITT Group 3 and Group 4 compression algorithms can only be used with bilevel data.

Group 3 compression can be specified together with several T.4-specific options: 1d for 1-dimensional encoding, 2d for 2-dimensional encoding, and fill to force each encoded scanline to be zero-filled so that the terminating EOL code lies on a byte boundary. Group 3-specific options are specified by appending a ``:''-separated list to the ``g3'' option; e.g. -c g3:2d:fill to get 2D-encoded data with byte-aligned EOL codes.

LZW, Deflate and LZMA2 compression can be specified together with a predictor value. A predictor value of 2 causes each scanline of the output image to undergo horizontal differencing before it is encoded; a value of 1 forces each scanline to be encoded without differencing. A value 3 is for floating point predictor which you can use if the encoded data are in floating point format. LZW-specific options are specified by appending a ``:''-separated list to the ``lzw'' option; e.g. -c lzw:2 for LZW compression with horizontal differencing.

Deflate and LZMA2 encoders support various compression levels (or encoder presets) set as character ``p'' and a preset number. ``p1'' is the fastest one with the worst compression ratio and ``p9'' is the slowest but with the best possible ratio; e.g. -c zip:3:p9 for Deflate encoding with maximum compression level and floating point predictor.

-f

Specify the bit fill order to use in writing output data. By default, ndpi2tiff will create a new file with the same fill order as the original. Specifying -f lsb2msb will force data to be written with the FillOrder tag set to LSB2MSB, while -f msb2lsb will force data to be written with the FillOrder tag set to MSB2LSB.

-i

Ignore non-fatal read errors and continue processing of the input file.

-l

Specify the length of a tile (in pixels). ndpi2tiff attempts to set the tile dimensions so that no more than 8 kilobytes of data appear in a tile.

-L

Force output to be written with Little-Endian byte order. This option only has an effect when the output file is created or overwritten and not when it is appended to.

-M

Suppress the use of memory-mapped files when reading images.

-p

Specify the planar configuration to use in writing image data that has one 8-bit sample per pixel. By default, ndpi2tiff will create a TIFF file with the same planar configuration as the original NDPI file. Specifying -p contig will force data to be written with multi-sample data packed together, while -p separate will force samples to be written in separate planes.

-r

Specify the number of rows (scanlines) in each strip of data written to the output file. By default (or when value 0 is specified), ndpi2tiff attempts to set the rows/strip that no more than 8 kilobytes of data appear in a strip. If you specify special value -1 it will results in infinite number of the rows per strip. The entire image will be the one strip in that case.

-s

Force the output file to be written with data organized in strips (rather than tiles).

-t

Force the output file to be written with data organized in tiles (rather than strips). options can be used to force the resultant image to be written as strips or tiles of data, respectively.

-w

Specify the width of a tile (in pixels). ndpi2tiff attempts to set the tile dimensions so that no more than 8 kilobytes of data appear in a tile.

-x

Force the output file to be written with PAGENUMBER value in sequence.

-,=character

substitute character for `,' in parsing image directory indices in files. This is necessary if filenames contain commas. Note that -,= with whitespace immediately following will disable the special meaning of the `,' entirely. See examples.

EXAMPLES

ndpi2tiff a.ndpi

The following converts a NDPI file into TIFF using LZW compression:

ndpi2tiff -c lzw a.ndpi

The following converts a NDPI file into TIFF using JPEG compression with quality 20%:

ndpi2tiff -c jpeg:20 a.ndpi

The following converts a NDPI file into a BigTIFF file (needed if the output file is larger than 4 GiB):

ndpi2tiff -8 a.ndpi

To extract a selected set of images from a NDPI file, the file name may be immediately followed by a `,' separated list of image directory indices. The first image is always in directory 0. Thus, to copy the 1st and 3rd images of image file ``a.ndpi'' to ``a.tif'':

ndpi2tiff a.ndpi,0,2

A trailing comma denotes remaining images in sequence. The following command will convert all image with except the first one:

ndpi2tiff a.ndpi,1,

As a special case, to extract from a NDPI file only the microscopic images (thus ignore the macroscopic image(s) or map(s)), option -m can be given:

ndpi2tiff -m a.ndpi

BUGS

If the output TIFF file is larger than 4 GiB and the option -8 was not given, fails with error messages instead of starting again, writing a BigTIFF file, or at least advising to use the option -8

SEE ALSO

ndpisplit(1), tiffmakemosaic(1), tifffastcrop(1), tiffsplit(1), tiffcrop(1), libtiff(3TIFF)

Home Page

http://www.imnc.in2p3.fr/pagesperso/deroulers/software/ndpitools/

AUTHOR

Christophe Deroulers

Reuse parts of LibTIFF's tiffcp. LibTIFF is copyright (c) 1988-1997 Sam Leffler and copyright (c) 1991-1997 Silicon Graphics, Inc.

Index

NAME

USAGE

DESCRIPTION

OPTIONS

EXAMPLES

BUGS

SEE ALSO

AUTHOR