What is it?

Dapple is designed to work with microarrays on glass. The spot-finding techniques used are robust to uneven spot sizes and positional deviations caused by "wobbling" of the arraying robot, as well as image noise and artifacts. As long as your spots are consistently circular, Dapple has a good chance of finding them accurately.

Dapple judges the quality of putative spots automatically using a classifier trained to match the investigator's judgement. In other words, it attempts to replicate the decisions you would make, based on visual inspection of the array, about whether to keep or reject each spot. The inferred qualities of spots are displayed visually, so that the investigator can focus on evaluating a few potentially erroneous spots rather than having to inspect the entire array.

More detailed information on Dapple's methods is available in the technical report UWTR 2000-08-05, available below.

• Dapple tech report: PDF (189 KB), Postscript (346 KB gzip'd)

Philosophy

I hope that you find Dapple to be useful, but I doubt it will be perfectly adapted to your arraying system. Instead of trying to handle all possible variations from one lab to another, I have tried to make Dapple as flexible as possible. In particular, you are free to modify the source code to meet your needs, or extract pieces to add to your own spot finding program. I and my users are interested in incorporating your bug fixes and extensions into the code!

Implementation and Licensing

The version of Dapple available on this page is distributed under the GNU General Public License, which is mandated by its use of FFTW. If you are interested in using Dapple but don't want to be bound by the GPL's redistribution requirements, UW's Office of Technology Transfer / Software and Copyright Ventures can work out alternate licensing terms. It should be possible to do a more liberal "free for noncommercial use" license provided that someone pays my costs to buy non-Open Source licenses for Qt and FFTW.

Common Complaints

I can't build Dapple with a non-GNU make!

I can't build Dapple with my local C++ compiler!

If you're using an older C++ compiler that doesn't handle extensive template usage well, upgrade to a recent version of g++. A recent release of DEC C++ should be OK on Alpha machines. Also, don't forget that you must compile Dapple with the same compiler that was used to build Qt! Otherwise, you may get interesting linking or runtime errors.

Get it!

• Dapple 0.86beta source code

• Dapple 0.85 source code

• Dapple 0.831 source code

• Dapple 0.81 source code
• Dapple 0.81 binary for Linux

• Support 8-bit TIFF files.
• Makefile overhaul to simplify configuration of paths and options, and to avoid gratuitous dependence on GNU-specific features.
• Fix some minor bugs that prevented building under gcc 3.0.
• Fix an insidious bug that caused intermittent crashes when loading images!

• sundry bug fixes
• Correctly read both compressed and uncompressed TIFFs.
• Reduce peak memory usage, both in the program itself and in the X server.
• Switch to using integer-valued pixels internally, so that we can easily switch between 16 and 32 bpp. The pixel size can be set at compile time by the -DSMALL_PIXELS flag, which is on by default (implying 16 bits of internal resolution).
• Attempt to catch common out-of-memory conditions that occur with really large array images, instead of just crashing.

• support for single-channel images
• ability to correct misregistration between image channels interactively prior to grid placement and spot finding
• support for reading generic 16-bit linear TIFFs as well as GEL files
• removal of all known source incompatibilities with ANSI standard C/C++ (compiles without warnings using g++ 2.95.2 -Wall -ansi -pedantic, and with no serious warnings on DEC cxx -Wall -ansi)
• code cleanup, particularly in image loading, which should make it easier to add new image formats
• miscellaneous bug fixes

Who am I?