Dataset Information

Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics.

ABSTRACT: Time-lapse cameras facilitate remote and high-resolution monitoring of wild animal and plant communities, but the image data produced require further processing to be useful. Here we publish pipelines to process raw time-lapse imagery, resulting in count data (number of penguins per image) and 'nearest neighbour distance' measurements. The latter provide useful summaries of colony spatial structure (which can indicate phenological stage) and can be used to detect movement - metrics which could be valuable for a number of different monitoring scenarios, including image capture during aerial surveys. We present two alternative pathways for producing counts: (1) via the Zooniverse citizen science project Penguin Watch and (2) via a computer vision algorithm (Pengbot), and share a comparison of citizen science-, machine learning-, and expert- derived counts. We provide example files for 14 Penguin Watch cameras, generated from 63,070 raw images annotated by 50,445 volunteers. We encourage the use of this large open-source dataset, and the associated processing methodologies, for both ecological studies and continued machine learning and computer vision development.

SUBMITTER: Jones FM

PROVIDER: S-EPMC7099010 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics.

Jones Fiona M FM Arteta Carlos C Zisserman Andrew A Lempitsky Victor V Lintott Chris J CJ Hart Tom T

Scientific data 20200326 1

Time-lapse cameras facilitate remote and high-resolution monitoring of wild animal and plant communities, but the image data produced require further processing to be useful. Here we publish pipelines to process raw time-lapse imagery, resulting in count data (number of penguins per image) and 'nearest neighbour distance' measurements. The latter provide useful summaries of colony spatial structure (which can indicate phenological stage) and can be used to detect movement - metrics which could b ...[more]

PMID: 32218449

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Project description:The emergence of new digital technologies has enabled a new way of doing research, including active collaboration with the public ('citizen science'). Innovation in machine learning (ML) and natural language processing (NLP) has made automatic analysis of large-scale text data accessible to study individual perspectives in a convenient and efficient fashion. Here we blend citizen science with innovation in NLP and ML to examine (1) which categories of life events persons with multiple sclerosis (MS) perceived as central for their MS; and (2) associated emotions. We subsequently relate our results to standardized individual-level measures. Participants (n = 1039) took part in the 'My Life with MS' study of the Swiss MS Registry which involved telling their story through self-selected life events using text descriptions and a semi-structured questionnaire. We performed topic modeling ('latent Dirichlet allocation') to identify high-level topics underlying the text descriptions. Using a pre-trained language model, we performed a fine-grained emotion analysis of the text descriptions. A topic modeling analysis of totally 4293 descriptions revealed eight underlying topics. Five topics are common in clinical research: 'diagnosis', 'medication/treatment', 'relapse/child', 'rehabilitation/wheelchair', and 'injection/symptoms'. However, three topics, 'work', 'birth/health', and 'partnership/MS' represent domains that are of great relevance for participants but are generally understudied in MS research. While emotions were predominantly negative (sadness, anxiety), emotions linked to the topics 'birth/health' and 'partnership/MS' was also positive (joy). Designed in close collaboration with persons with MS, the 'My Life with MS' project explores the experience of living with the chronic disease of MS using NLP and ML. Our study thus contributes to the body of research demonstrating the potential of integrating citizen science with ML-driven NLP methods to explore the experience of living with a chronic condition.

Project description:BackgroundThe increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that are efficient, publicly available and easy to use. Such tools are starting to be developed for a wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research.New informationThis paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.

Dataset Information

Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics.

Publications

Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics.

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