SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects


Contact
Bank.Beszteri [ at ] awi.de

Abstract

Background Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleoenvironmental studies. In these applications, usually large numbers of frustules need to be identified and / or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.



Item Type
Article
Authors
Divisions
Primary Division
Programs
Primary Topic
Publication Status
Published
Eprint ID
35825
DOI 10.1186/1471-2105-15-218

Cite as
Kloster, M. , Kauer, G. and Beszteri, B. (2014): SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects , BMC Bioinformatics, 15 , p. 218 . doi: 10.1186/1471-2105-15-218


Share
Add to AnyAdd to TwitterAdd to FacebookAdd to LinkedinAdd to PinterestAdd to Email


Citation

Geographical region
N/A

Research Platforms
N/A

Campaigns
N/A


Actions
Edit Item Edit Item