ImageJ plugin for automatic segmentation of seeds from blue background images
Alessandra Mendes, Andrea Loddo
This plugin is part of the scientific paper "A new automatic approach to seed image analysis: From acquisition to segmentation", realised by the following authors.
Authors: Vale A.M.P.G. 1 , Ucchesu M. 2* , Di Ruberto C. 3 , Loddo A. 3 , Soares J.M. 4 , Bacchetta G. 2,5
1 Escola Agrícola de Jundiaí (EAJ), Universidade Federal do Rio Grande do Norte (UFRN), Rodovia RN 160, Km 03, CEP 59280-000 Macaíba (RN), Brasil.
2 Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università degli Studi di Cagliari, Viale S. Ignazio da Laconi 13, 09123 Cagliari, Italy.
3 Dipartimento di Matematica e Informatica, Università degli Studi di Cagliari, Via Ospedale 72, 09124 Cagliari, Italy.
4 Universidade Federal do Rio Grande do Norte (UFRN), Rodovia RN 160, Km 03, CEP 59280-000 Macaíba (RN), Brasil.
5 Hortus Botanicus Karalitanus (HBK), Università degli Studi di Cagliari, Viale S. Ignazio da Laconi 11, 09123 Cagliari, Italy.
The manuscript mentioned above described in detail the plugin's workflow.
For the sake of simplicity: it works on an entire folder of digital seed images, acquired with a blue background.
It requires the user to indicate one file among the several which can present inside a folder (the folder MUST contain only blue background images) and, after the pre-processing and segmentation phase, produces a ResultTable inside ImageJ with some statistical data and, above all, saves original color, gray-level, and black and white mask images under the folder "results", on the same folder containing the images.
E.g.: if the folder containing the images is in C:\Users\User\Desktop\Seeds -> the results will be in C:\Users\User\Desktop\Seeds\results