In 2008 I started a manual which will try to bring together information about installing and using these tools. It is currently at:

  http://86.22.72.242:8080/dokuwiki/doku.php?id=warping_manual:start

Please get in touch with Greg if you would like write access to contribute - I would be delighted!  Note that there has been a change of web address since November 2008 when I had to move my server. I hope to have the server at a new permanent location by Spring 2009, most likely flybrain.mrc-lmb.cam.ac.uk .  Sorry for any inconvenience.

Some of the advantages of the nrrd format (nearly raw raster data) include.

1. Simple ascii header and raw image data
2. Implemented either in single combined .nrdd file or a .nhdr header file pointing to 1 or more data files
3. Same format includes well defined way to handle complex data (eg vectors and tensors)
4. A white space separated text file of numbers is also a nrrd file!
5. Handles all critical metadata including spatial calibration, axis definitions (including world axes and image axes)
6. Can handle voxels considered as single points or small cubic volumes (cell vs node)
7. Can handle arbitrary key, value tags to record additional information
8. Can use compressed data e.g. gzip
9. Header can contain comment lines starting with a #
10. Open source cross-platform C IO library available to link into your applications
11. I have written simple open source (LGPL) Java plugins to read and write images with ImageJ.
12. Separate header files can be used to turn almost any 'raw' image file format into a Nrrd compatible file
13. eg I have provided a perl script bioradinfo.pl below that can turn a whole tree of Biorad PIC files into nrrd readable files just by writing an additional header file.
14. Medical imaging projects such as NA-MIC have adopted nrrd format and integrated it into ITK.
15. There is a command line tool unu which provides a great many useful image operations for the nrrd format.

Disadvantages:

I would like to propose the Nearly Raw Raster Data format (NRRD) developed by Gordon Kindlmann as an interchange format for Drosophila (and other) neuroanatomy image data. Nrrd is a simple format that consists of an ascii header followed by image (or other raster) data in raw, text or compressed format. If required the header can be written as a separate file from the image.

This format has a number of useful features that I have listed here . The key advantages over a format like tiff seem to me include: simplicity, a standardised way to handle critical spatial metadata (world and image axes etc), no immediate restrictions on data size per file, provides a way to keep track of data spread data over multiple files, the ability to write a header file of a few lines that can turn many image files (raw, PGM, PPM, Biorad PIC, AmiraMesh) into a nrrd-compatible file. For example this is a nrrd header for a Biorad file:

NRRD0004
# Created by Nrrd_Writer at Thu Apr 05 17:49:22 BST 2007
type: uint8
encoding: gzip
endian: little
dimension: 3
sizes: 512 512 88
spacings: 0.32964843 0.32964843 1.0
centers: cell cell cell
units: "microns" "microns" "microns"
byte skip: 76
data file: average-goodbrains-warp40-5_e1e-2.PIC.gz

Finally the point of an interchange format is not that you have to use it for all your day to day activities. Rather it should be a read and write option for your data that encapsulates all critical metadata and allows a wide spectrum of other users to exchange information. Of course you can now convert any of your image data to Nrrd using the ImageJ plugins below. ImageJ can open over 40 different file formats including Tiff, confocal stacks from Zeiss LSM, Leica, Nikon and Olympus microscopes, AmiraMesh, raw etc.

Program Files