Download

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.

Pre-compiled binaries

64-bit Windows: ndpi2tiff.exe
ndpisplit.exe ndpisplit-m.exe ndpisplit-mJ.exe ndpisplit-s.exe ndpisplit-s-m.exe ndpisplit-s-mJ.exe
32-bit Windows: ndpi2tiff.exe
ndpisplit.exe ndpisplit-m.exe ndpisplit-mJ.exe ndpisplit-s.exe ndpisplit-s-m.exe ndpisplit-s-mJ.exe
Mac OS 10.6 and later: Pkg installer
Linux x86_64: ndpi2tiff   ndpisplit

ImageJ plugins

NDPITools_.jar

Source code

NDPITools   ImageJ plugins

NDPITools

Version française

About

Using a Hamamatsu slide scanner such as the NanoZoomer, you may end up with NDPI files that can't always be directly open in standard image analysis software such as ImageJ. NDPITools is a collection of software that can convert NDPI files to standard TIFF files, possibly cutting them into smaller JPEG or TIFF pieces that will better fit into your computer's memory. It comes with a bundle of plugins for ImageJ which enable the use of the software directly inside ImageJ with point-and-click.

Download

The software is open source, distributed under the GNU General Public License v. 3.0 or any later version, at your option. It is based on the libtiff, libjpeg , and 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.

Installation

For the NDPITools ImageJ plugins:

Put the file NDPITools_.jar into the plugins directory of ImageJ (you can find out its location by selecting Plugins -> Utilities -> ImageJ Properties in ImageJ's menus). Look for the value of the tag Menus.getPlusInsPath near the middle of the displayed Properties window.

For the NDPITools software:

If you only use them through the ImageJ plugins, you can put their files at the same location as NDPITools_.jar (see above).

In the general case, under Mac OS X or Linux, you can copy or move the files to a directory listed in your PATH, e.g. /usr/local/bin. Under Mac OS X, this will be done automatically if you install from the .pkg file.

Using the software

To use the ImageJ NDPITools plugins, you can read the specific instructions. The rest of this page deals mainly with the command line NDPITools.

Under Windows, you can simply drag and drop a NDPI file over the .exe file or icon of the program you want to use.

ndpisplit and ndpi2tiff should succeed even on computers having not too much memory.

On all platforms (including Windows, Linux, Mac OS X), you can also launch the programs 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 NDPI file (under Mac OS X, the default path is /usr/local/bin). The resulting TIFF or JPEG file(s) will be produced in the directory where the NDPI file resides. Only one NDPI file at a time maybe given on the command line.

We have been advised that .exe files may cause some problems with antivirus software under Windows, especially when launched from ImageJ. The .exe files we publish should be virus-free since they have been made under Unix thanks to MinGW and MinGW-w64. We had no trouble using them with the Avira antivirus under Windows XP.

ndpisplit options to deal with huge images

Quite often, the resulting images at largest magnifications (x20 or x40) will be so huge that they won't fit into memory and, therefore, can't be open with standard software. E.g., the image of a piece of tissue of 1 square centimeter scanned at 40x typically takes 5 Gib of memory. To address this problem, ndpisplit can be run with the options below. For your convenience, we provide in the download section variants of ndpisplit where options have been turned-on by default: e.g., running ndpisplit-mJ.exe is like running ndpisplit with the -mJ option. Otherwise, you can run the programs from a command line and give options after the command name, separated by spaces.

See also the full list of options to ndpisplit.

Opening the TIFF files with ImageJ

In its versions up to 1.47, core ImageJ is not able to open TIFF files which use JPEG compression. However:

Are maximal resolution images too large for ImageJ?

Core ImageJ, in its versions up to 1.47, can't open images which have more than 2 billions pixels (2^31). That happens even if you increase the available memory: it is due to an intrinsic limitations to Java arrays, addressed through 32-bits signed integers. (If your image is not that large, you can increase ImageJ's memory using Edit->Options->Memory).

In that case, you may:

Behind the scene

The main reason why standard software can't open NDPI files, although NDPI files look internally quite close to TIFF files, is that the largest images inside a NDPI file can be more that 65500 pixels wide or high, whereas the JPEG standard used to compress and decompress them limits the dimensions to 65535 (there are also additional difficulties on 32 bits operating systems). The NDPITools use a special version of libjpeg and a modifed version of libtiff to overcome this and translate NDPI files into more standard TIFF files.

Changelog

Other software

As of July 2011, the LOCI bio-formats ImageJ plugin is able to open NDPI files that contain no image wider or higher than 65500 pixels. (The NDPItools are useful to overcome this limit).

OpenSlide is a library software aiming at opening under a unified framework all virtual microscopy images (slides) formats. It is able to open some of the Hamamatsu formats.

Software and projects which use the NDPITools

Credits and acknowledgments

This software was developed by the modelling team of the IMNC laboratory near Paris, France, during a research project funded by the IN2P3 and INSB Institutes of the CNRS and by the Universities Paris Diderot-Paris 7 and Paris South-11.

We thank the Laboratory of Pathology of the Saint-Louis Hospital in Paris (France) (especially Philippe Bertheau, David Ameisen and Fatiha Bouhidel) for the kind access to their slide scanners, and Marc Lartaud and Alexandre Granier from Montpellier RIO Imaging, Christophe Klein from the Cordeliers Research Center, Chloé Gerin now at the IPN and at IDES, and Philippe Mailly from the CIRB for tests, bug reports, and suggesting improvements.

The NDPITools are the topic of a PLUME index card. Thanks to the PLUME!

Contact: Christophe Deroulers

Hamamatsu, NanoZoomer, Linux, Mac OS X and Windows are registered trademarks of their respective owners.

Valid HTML 4.01 Transitional