Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates

Amir, Corinne; Oliver, Thomas; Lamirand, Mia; Couch, Courtney

doi:10.25923/s2ym-tn10

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Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates

2023
By Amir, Corinne ; Oliver, Thomas ; Lamirand, Mia ; ...
Series: NOAA technical memorandum NMFS PIFSC ; 139

[PDF-4.70 MB]

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Personal Author:

Amir, Corinne ; Oliver, Thomas ; Lamirand, Mia ; Couch, Courtney

Amir, Corinne ; Oliver, Thomas ; Lamirand, Mia ; Couch, Courtney Less -
Corporate Authors:

Pacific Islands Fisheries Science Center (U.S.). ; Cooperative Institute for Marine and Atmospheric Research.

Pacific Islands Fisheries Science Center (U.S.). ; Cooperative Institute for Marine and Atmospheric Research. Less -
NOAA Program & Office:

NMFS (National Marine Fisheries Service) ; PIFSC (Pacific Islands Fisheries Science Center) ; CIMAR (Cooperative Institute for Marine and Atmospheric Research) ; CoRIS (Coral Reef Information System)

NMFS (National Marine Fisheries Service) ; PIFSC (Pacific Islands Fisheries Science Center) ; CIMAR (Cooperative Institute for Marine and Atmospheric Research) ; CoRIS (Coral Reef Information System) Less -
Description:

Photogrammetry, a method of producing geometrically accurate large area imagery, has increased in popularity as a tool for studying spatio-temporal trends on coral reefs. Large area image analysis reduces costs and complexity of field operations, provides a permanent record of benthic communities, and can be used to track hundreds to thousands of coral colonies across multiple sites and time points, thus providing the ecological and spatial replication necessary to test the links between vital rates and environmental conditions (Rodriguez et al. 2022). However, manually annotating imagery and tracking coral colonies across time is labor intensive, taking approximately 40 hours to annotate and link corals within ~10m2 of reef across two time points. Currently, fully manual annotation cannot keep up with the speed at which imagery is collected. To address this limitation, machine learning technologies have increased in popularity as a tool to reduce image annotation time while maintaining accuracy. One such example is TagLab, an open-source AI-assisted software created by the Visual Computing Lab (http://vcg.isti.cnr.it/) that uses a manually assisted workflow to semi-automatically annotate and track coral colonies across multiple time points (Pavoni et al. 2021). This document provides the standard operating procedures (SOP) for the integration of TagLab into our current vital rates workflow as outlined in Rodriguez et al. (2022).
Keywords:

[+]

Coral Reefs And Islands Handbooks, Manuals, Etc. Machine Learning Photogrammetry Vital Statistics
Series:

NOAA technical memorandum NMFS PIFSC ; 139
DOI:

https://doi.org/10.25923/s2ym-tn10
Format:

PDF
CoRIS Project ID:

CRCP Project ID ; 31360
Document Type:

Technical Memorandum
License:

https://creativecommons.org/publicdomain/zero/1.0/
Rights Information:

CC0 Public Domain
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Submitted
Main Document Checksum:

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urn:sha256:8a6c7fa6d8c662524f5bcc9eb5c7a3b3e6baa340393135ddc483ddc37d60aaff
Download URL:

https://repository.library.noaa.gov/view/noaa/50840/noaa_50840_DS1.pdf
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Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates

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