If you use this software for academic research, please quote:
Deroulers et al., Analyzing huge
pathology images with open source software, Diagnostic
Pathology 8:92 (2013).
And/or if you find this software
useful, please send us an email! This will
help us to get support from our funding agencies to keep working on it.
You can use following address (remove the anti-spam):
christophe.deroulers.nospam@univ-paris-diderot.fr.
| 64-bit Windows: | tiffmakemosaic.exe tiffmakemosaic-j.exe tifffastcrop.exe tiffsplittiles.exe |
| 32-bit Windows: | tiffmakemosaic.exe tiffmakemosaic-j.exe tifffastcrop.exe tiffsplittiles.exe |
LargeTIFFTools is a collection of software that can help managing (very) large TIFF files, especially files that are too large to fit entirely into your computer's memory. It is composed of the following programs:
tiffmakemosaic opens a
TIFF file and makes a mosaic out of it.tifffastcrop crops
(extracts) a rectangular region from a TIFF file without opening the
whole image into memory and saves it as a TIFF, JPEG or PNG
file.tiffsplittiles copies
the tiles of a tiled TIFF file into independent files (one for each
tile).The software is open source, distributed under the GNU General Public License v. 3.0. It uses noticeably the libtiff and libjpeg or libjpeg-turbo software, made free and open by its authors, which we acknowledge.
You can get the software through download (see the links in the frame). We provide some pre-compiled versions. The 32-bit Windows version should run under all versions of Windows (XP, Vista, 7; either 32- or 64-bits) but will produce images which require at most ca. 1 GiB memory. The 64-bit version goes beyond that limit.
If you install the software from source, you need the following
installed libraries: libtiff (we
recommend a version >= 4.0.0) and libjpeg (and possibly other
libraries that your version of libtiff might use, e.g. zlib). Basic instructions for installing from
source are: extract with tar xfj
<file>, compile and install with ./configure ; make ; make install.
Under Windows, you can simply drag and drop a TIFF (.tif) file over the .exe file or icon of the
relevant program. tiffmakemosaic.exe and
tiffsplittiles.exe will open the file and, if appropriate,
split it into multiple TIFF image files (while preserving the original).
tiffmakemosaic-j.exe does the same as tiffmakemosaic-j.exe, but stores the resulting
images into JPEG files (option -j is hardcoded). For options,
please refer to the documentation of each program for
details.
On all platforms (including Windows, Linux, Mac OS X), you can
also use it with a command line. Open a shell (e.g. command interpreter,
Terminal.app, xterm...) and launch the program by
typing its name (preceded by its path if needed) followed by a space
then the path to the TIFF file. The resulting TIFF or JPEG file(s) will
be produced in the directory where the original TIFF file resides.
A typical use is for anatomopathology or microscopy slide images, like the one that the NDPITools produce.
In principle, generating pieces from a large TIFF file can also be
achieved with several tools, as tiffcrop from the
libtiff, ImageMagick, and GraphicsMagick (one has to
first compute and specify explicitly the dimensions and positions of the
pieces, though). However, most of the software start with opening and
deciphering the whole image either in memory or in a huge temporary file
on the disk, which makes them quite slow or often unable to complete the
task by lack of memory.
In contrast, tiffmakemosaic, tifffastcrop and
tiffsplittiles avoid opening the whole image, which yields
speedup and guarantees successful termination of the process even on
computers with modest memory. Eg. to make a mosaic of 64 JPEG files
requesting less than 512 Mib of memory to open from a RGB image of
103168x63232 pixels, on a computer with 16 Gib of RAM and an i5 CPU,
tiffmakemosaic needs 2.5 minutes while GraphicsMagick needs 70
minutes.
tifffastcrop
is now able to deal with many bit-depths (e.g. RGB with alpha channel, or
1 bit-per-pixel black and white images, or 4 bits-per-pixel grayscale
images...) and to write PNG files in addition to TIFF and JPEG files. Now,
it tries to guess the output file format from the output filename, if
any.tifffastcrop
now supports Fax-like compression; corrected a bug in tiffmakemosaic in the case of
lossless compression and non-zero overlap.tifffastcrop and tiffmakemosaic of Fax-like
compression.tiffmakemosaic; new
options to handle TIFF files with multiple directories in tifffastcrop; support of WebP and
Zstd compression by both programs.tifffastcrop, fixed regression which
prevented to write JPEG files and fixed support of images with 2 or 4
bits per sample.tiffmakemosaic, added security for
the illegal case of zero-width or zero-length input image; modernised
code style.This software was developed by the modelling team of IJCLab (formerly IMNC) near Paris, France, during a research project funded by the IN2P3 and INSB Institutes of the CNRS and by Université de Paris (formerly the Paris Diderot-Paris 7 university) and the university Paris-Saclay (formerly the university Paris South-11).
Contact: Christophe Deroulers
Linux, Mac OS X and Windows are registered trademarks of their respective owners.