Journal Article

A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems

Lei Qu and Hanchuan Peng

in Bioinformatics

Volume 26, issue 8, pages 1091-1097
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI:

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology


Show Summary Details


Motivation: The fruit fly (Drosophila melanogaster) is a commonly used model organism in biology. We are currently building a 3D digital atlas of the fruit fly larval nervous system (LNS) based on a large collection of fly larva GAL4 lines, each of which targets a subset of neurons. To achieve such a goal, we need to automatically align a number of high-resolution confocal image stacks of these GAL4 lines. One commonly employed strategy in image pattern registration is to first globally align images using an affine transform, followed by local non-linear warping. Unfortunately, the spatially articulated and often twisted LNS makes it difficult to globally align the images directly using the affine method. In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem.

Results: We proposed to standardize a larval image by best aligning its principal skeleton (PS), and thus used this method as an alternative of the usually considered affine alignment. The PS of a shape was defined as a series of connected polylines that spans the entire shape as broadly as possible, but with the shortest overall length. We developed an automatic PS detection algorithm to robustly detect the PS from an image. Then for a pair of larval images, we designed an automatic image registration method to align their PSs and the entire images simultaneously. Our experimental results on both simulated images and real datasets showed that our method does not only produce satisfactory results for real confocal larval images, but also perform robustly and consistently when there is a lot of noise in the data. We also applied this method successfully to confocal images of some other patterns such as the adult fruit fly VNC and center brain, which have more complicated PS. This demonstrates the flexibility and extensibility of our method.

Availability: The supplementary movies, full size figures, test data, software, and tutorial on the software can be downloaded freely from our website


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4663 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.