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Measuring shoot length of submerged aquatic plants using graph analysis

Abstract

The fate of herbicides in experimental studies can be observed by measuring the total shoot lenght of submerged aquatic plants, such as M. spicatum and E. canadensis. manual measurement of the shoot lengths takes a lot of time and is difficult to trace. An ImageJ application has been develloped to measure the individual shoot length of the plants taken by a digital picture.

After thresholding the picture, the binary image is transferred to a skeleton and the skeleton to a weighted graph using the ImageJ plug-in Analyze-Skeleton (http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start).

The nodes in the graph are the junction pixels and the edges are the slab pixels. The weight of the edges corresponds with their length.

In computer science, the Floyd–Warshall algorithm is a graph analysis algorithm for finding shortest paths in a weighted graph. A single execution of the algorithm will find the lengths (summed weights) of the shortest paths between all pairs of vertices. The longest length can be considered as a good estimation of the total length of the plant.

The warshall algorithm was implemented in the Analyze-Skeleton plugin and used to measure the length of a large number of plants of both specimens.

The lengths measured this way were compared with manual measurements. The R2 was 0.95 for E. canadensis and 0.91 for M. spicatum. From those high R2 values we can conclude that the algorithm works very well.

Keywords

graph analysis, skeleton, shortest path, warshall

Administrative data

Presenting author: G. Polder
Organisation: Wageningen UR (University & Research centre)

co-authors: H.L.E. Hovens (Eindhoven University of Technology), A.J. Zweers (Wageningen UR)

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