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Conference proceeding
Automatic Metadata Generation for Fish Specimen Image Collections
2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL)
Sep 2021
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Metadata are key descriptors of research data, particularly for researchers seeking to apply machine learning (ML) to the vast collections of digitized specimens. Unfortunately, the available metadata is often sparse and, at times, erroneous. Additionally, it is prohibitively expensive to address these limitations through traditional, manual means. This paper reports on research that applies machine-driven approaches to analyzing digitized fish images and extracting various important features from them. The digitized fish specimens are being analyzed as part of the Biology Guided Neural Networks (BGNN) initiative, which is developing a novel class of artificial neural networks using phylogenies and anatomy ontologies. Automatically generated metadata is crucial for identifying the high-quality images needed for the neural network's predictive analytics. Methods that combine ML and image informatics techniques allow us to rapidly enrich the existing metadata associated with the 7,244 images from the Illinois Natural History Survey (INHS) used in our study. Results show we can accurately generate many key metadata properties relevant to the BGNN project, as well as general image quality metrics (e.g. brightness and contrast). Results also show that we can accurately generate bounding boxes and segmentation masks for fish, which are needed for subsequent machine learning analyses. The automatic process outperforms humans in terms of time and accuracy, and provides a novel solution for leveraging digitized specimens in ML. This research demonstrates the ability of computational methods to enhance the digital library services associated with the tens of thousands of digitized specimens stored in open-access repositories worldwide.
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Details
- Title
- Automatic Metadata Generation for Fish Specimen Image Collections
- Creators
- Joel Pepper - Drexel University,Department of Computer Science,Philadelphia,PA,USAJane Greenberg - Drexel UniversityYasin Bakis - Biodiversity Research Institute Tulane University,New Orleans,LA,USAXiaojun Wang - Biodiversity Research Institute Tulane University,New Orleans,LA,USAHenry Bart - Biodiversity Research Institute Tulane University,New Orleans,LA,USADavid Breen - Drexel University
- Publication Details
- 2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL)
- Publisher
- IEEE
- Grant note
- #1940233,#1940322 / NSF (10.13039/100000001)
- Resource Type
- Conference proceeding
- Language
- English
- Academic Unit
- Information Science; Computer Science
- Web of Science ID
- WOS:000760315700004
- Scopus ID
- 2-s2.0-85124177645
- Other Identifier
- 991019168454404721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Computer Science, Interdisciplinary Applications
- Information Science & Library Science