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.

You can download the Java plugins below. Copy the .class files into your ImageJ plugins folder and restart ImageJ. These plugins are still developmental but they will read and write 2D and 3D single channel data in either raw or gzip compressed format. Comments welcome to jefferis@gmail.com.