Talk:Embryology Image Tutorial

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Cite this page: Hill, M.A. (2019, June 19) Embryology Embryology Image Tutorial. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Talk:Embryology_Image_Tutorial

2011

Figure text extraction in biomedical literature

Kim D, Yu H.

PLoS One. 2011 Jan 13;6(1):e15338.

Abstract

BACKGROUND: Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures.

METHODOLOGY: We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons.

RESULTS/CONCLUSIONS: The evaluation on 382 figures (9,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search.

PMID: 21249186 http://www.ncbi.nlm.nih.gov/pubmed/21249186

2010

Automatic figure ranking and user interfacing for intelligent figure search

Yu H, Liu F, Ramesh BP. PLoS One. 2010 Oct 7;5(10):e12983. PMID: 20949102

2009

Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension

Yu H, Agarwal S, Johnston M, Cohen A. J Biomed Discov Collab. 2009 Jan 6;4:1. PMID: 19126221


FigSum: automatically generating structured text summaries for figures in biomedical literature

Agarwal S, Yu H. AMIA Annu Symp Proc. 2009 Nov 14;2009:6-10. PMID: 20351812