Published

Counting using deep learning regression gives value to ecological surveys. Version 19

Royal Netherlands Institute for Sea Research https://doi.org/10.25850/nioz/7b.b.0c

Many ecological studies rely on count data and involve manual counting of objects of interest, which is time-consuming and especially disadvantageous when time in the field or lab is limited. However, an increasing number of works uses digital imagery, which opens opportunities to automatise counting tasks. In this study, we use machine learning to automate counting objects of interest without the need to label individual objects. By leveraging already existing image-level annotations, this approach can also give value to historical data that were collected and annotated over longer time series (typical for many ecological studies), without the aim of deep learning applications. We demonstrate deep learning regression on two fundamentally different counting tasks: (i) daily growth rings from microscopic images of fish otolith (i.e., hearing stone) and (ii) hauled out seals from highly variable aerial imagery. In the otolith images, our deep learning-based regressor yields an RMSE of 3.40 day-rings and an R^2 of 0.92. Initial performance in the seal images is lower (RMSE of 23.46 seals and R^2 of 0.72), which can be attributed to a lack of images with a high number of seals in the initial training set, compared to the test set. We then show how to improve performance substantially (RMSE of 19.03 seals and R^2 of 0.77) by carefully selecting and relabelling just 100 additional training images based on initial model prediction discrepancy. The regression-based approach used here returns accurate counts (R^2 of 0.92 and 0.77 for the rings and seals, respectively), directly usable in ecological research.

Data and Resources

Additional Info

Field	Value
Subject	Earth and Environmental Sciences
DAS Code	7b.b.0c
Source	https://dataportal.nioz.nl/doi/10.25850/nioz/7b.b.0c
Version	19
Creator(s)	Hoekendijk, Jeroen (Royal Netherlands Institute for Sea Research) Contact the corresponding author
Depositor	Jeroen Hoekendijk
Publication Date	2021-12-01
Deposit Date	2021-11-01
Dataset Persistent Identifier	DOI:10.25850/nioz/7b.b.0c
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Related identifier
Contributor	NIOZ Royal Netherlands Institute for Sea Research
Distributor	Research Data Management(NIOZ Royal Netherlands Institute for Sea Research)
Distribution Date	2021-11-01
Production Date	2021-12-01
Dates	[]
Funding References	NWO (project ALWPP.2017.003)
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