Comparative Evaluation of Free Web Tools ImageJ and Photopea for the Surface Area Quantification of Planar Substrates and Organisms

El-Khaled, Yusuf C.; Lago, Alexandra Kler; Mezger, Selma D.; Wild, Christian

doi:10.3390/d14040272

Cited by 5 publications

(6 citation statements)

References 15 publications

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“…Surface area was calculated in ImageJ (Schneider et al, 2012 ) by using cylindrical surface area (SA = 2πrh + 2πr 2 ) as a proxy for individual branches within a ramet. It has been previously demonstrated that software such as ImageJ can be used for accurate surface area measurements on organisms with complex and irregular shapes, by breaking down parts into geometric figures for analysis (El‐Khaled et al, 2022 ; McLachlan et al, 2022 ; McLachlan & Grottoli, 2021 ). We further evaluated this metric by comparing ImageJ surface area values versus wax dipping (Veal et al, 2010 ), in an independent set of 50 A. hyacinthus coral fragments.…”

Section: Methodsmentioning

confidence: 99%

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

Walker

Nestor

Golbuu

et al. 2022

Evolutionary Applications

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The prevalence of global coral bleaching has focused much attention on the possibility of interventions to increase heat resistance. However, if high heat resistance is linked to fitness tradeoffs that may disadvantage corals in other areas, then a more holistic view of heat resilience may be beneficial. In particular, overall resilience of a species to heat stress is likely to be the product of both resistance to heat and recovery from heat stress. Here, we investigate heat resistance and recovery among individual Acropora hyacinthus colonies in Palau. We divided corals into low, moderate, and high heat resistance categories based on the number of days (4–9) needed to reach significant pigmentation loss due to experimental heat stress. Afterward, we deployed corals back onto a reef in a common garden 6‐month recovery experiment that monitored chlorophyll a , mortality, and skeletal growth. Heat resistance was negatively correlated with mortality during early recovery (0–1 month) but not late recovery (4–6 months), and chlorophyll a concentration recovered in heat‐stressed corals by 1‐month postbleaching. However, moderate‐resistance corals had significantly greater skeletal growth than high‐resistance corals by 4 months of recovery. High‐ and low‐resistance corals on average did not exhibit skeletal growth within the observed recovery period. These data suggest complex tradeoffs may exist between coral heat resistance and recovery and highlight the importance of incorporating multiple aspects of resilience into future reef management programs.

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Section: Methodsmentioning

confidence: 99%

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

Walker

Nestor

Golbuu

et al. 2022

Evolutionary Applications

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“…Determination of the final object shrinkage on the slice button mushroom is determined based on the surface area. Surface area analysis using ImageJ 1.8.0-172 software [14,15]. The final large percentage of dried mushroom slices can be determined by the following equation ( 3), where Sa is the final object shrinkage and h t-i is the t-th and 0-th data (initial).…”

Section: Surface Areamentioning

confidence: 99%

Vacuum Application with Water Jet Technology in Drying Button Mushrooms (Agaricus bisporus)

Hawa¹,

Efendi²,

Habibah³

2023

fst

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Button mushroom (Agaricus bisporus) is the most popular mushroom commodity in the world because of its deliciousness, texture, and nutritional value. However, the high water content in this product makes it perishable so that drying as a preservation method is needed. The present study aims to evaluate the vacuum drying method based on water jet technology by observing the physical quality and drying kinetics of slice button mushrooms. Drying was controlled with a constant pressure of 130 mbar with temperature variations of 50, 60, and 70 o C. The sample used was slice button mushroom with a thickness of 5 mm which was blanched in ascorbic acid solution. The results showed that vacuum drying can reduce water content up to 6.01-15.15 % (w.b.) with an average drying rate of 0.17-0.18 % (w.b.)/min. ANOVA test showed that the variation of drying temperature and blanching treatment had a significant effect on all observed physical parameters (moisture content, surface area, hardness, and color). At the end of drying, changes in physical parameters were observed, including surface area (19.98-38.45%), hardness (54.45-536.95 g), and color with indicators L* (25.45-71.01), a* (-2.52-15.44), and b* (5.63-29.38), whiteness (22.11-71.19%), and the best drying kinetics prediction models are the Two-term and Wang-Singh models.

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“…Many studies of coral reefs have implemented manual tracing of coral colonies to estimate their areal footprint as a 2D surface, which is used as a proxy for colony size [22][23][24][25]43]. By approximating the 3D surface areas of corals, we captured a loss rate of live coral that was significantly greater than that estimated by 2D planar area (Figure 7).…”

Section: Quantification Of the Coral Bleaching Eventmentioning

confidence: 99%

“…However, efficiently extracting biological metrics, such as cover of benthic organisms (e.g., coral or algae), can be more complicated and time-consuming [6]. A widely implemented approach is image segmentation-the scaled measurement and annotation of objects within an image [22][23][24][25]. This form of image analysis is generally used to estimate metrics, including percentage cover of benthic flora and fauna, via the 2D areal footprint of organisms in a given area.…”

Section: Introductionmentioning

confidence: 99%

Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation

Kopecky,

Pavoni,

Nocerino

et al. 2023

Remote Sensing

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Detecting the impacts of natural and anthropogenic disturbances that cause declines in organisms or changes in community composition has long been a focus of ecology. However, a tradeoff often exists between the spatial extent over which relevant data can be collected, and the resolution of those data. Recent advances in underwater photogrammetry, as well as computer vision and machine learning tools that employ artificial intelligence (AI), offer potential solutions with which to resolve this tradeoff. Here, we coupled a rigorous photogrammetric survey method with novel AI-assisted image segmentation software in order to quantify the impact of a coral bleaching event on a tropical reef, both at an ecologically meaningful spatial scale and with high spatial resolution. In addition to outlining our workflow, we highlight three key results: (1) dramatic changes in the three-dimensional surface areas of live and dead coral, as well as the ratio of live to dead colonies before and after bleaching; (2) a size-dependent pattern of mortality in bleached corals, where the largest corals were disproportionately affected, and (3) a significantly greater decline in the surface area of live coral, as revealed by our approximation of the 3D shape compared to the more standard planar area (2D) approach. The technique of photogrammetry allows us to turn 2D images into approximate 3D models in a flexible and efficient way. Increasing the resolution, accuracy, spatial extent, and efficiency with which we can quantify effects of disturbances will improve our ability to understand the ecological consequences that cascade from small to large scales, as well as allow more informed decisions to be made regarding the mitigation of undesired impacts.

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Comparative Evaluation of Free Web Tools ImageJ and Photopea for the Surface Area Quantification of Planar Substrates and Organisms

Cited by 5 publications

References 15 publications

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

Vacuum Application with Water Jet Technology in Drying Button Mushrooms (Agaricus bisporus)

Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation

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