A new tool for 3D segmentation of computed tomography data:<i>Drishti Paint</i>and its applications

Hu, Yuzhi; Limaye, Ajay; Lü, Jing

doi:10.1101/2020.04.09.997965

Cited by 3 publications

(3 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Microtomography (µCT) scans of shells from mussels (M. trossulus) included in OA treatments were taken using a Skyscan 1076 scanner (Bruker, Billerica, MA, USA), imaging shells in 35 µm slices at 45 kV. Three-dimensional image reconstruction was performed in NRecon (Micro Photonics Inc., Allentown, PA, USA), with further rendering in Drishti [81]. A 1 mm diameter cylinder was placed on the drill hole of each shell and used to record the mean and maximum grayscale values of scan slices in aggregate.…”

Section: Sem and µCt Imagingmentioning

confidence: 99%

Mussels Repair Shell Damage despite Limitations Imposed by Ocean Acidification

George

O’Donnell

Concodello

et al. 2022

JMSE

View full text Add to dashboard Cite

Bivalves frequently withstand shell damage that must be quickly repaired to ensure survival. While the processes that underlie larval shell development have been extensively studied within the context of ocean acidification (OA), it remains unclear whether shell repair is impacted by elevated pCO2. To better understand the stereotypical shell repair process, we monitored mussels (Mytilus edulis) with sublethal shell damage that breached the mantle cavity within both field and laboratory conditions to characterize the deposition rate, composition, and integrity of repaired shell. Results were then compared with a laboratory experiment wherein mussels (Mytilus trossulus) repaired shell damage in one of seven pCO2 treatments (400–2500 µatm). Shell repair proceeded through distinct stages; an organic membrane first covered the damaged area (days 1–15), followed by the deposition of calcite crystals (days 22–43) and aragonite tablets (days 51–69). OA did not impact the ability of mussels to close drill holes, nor the microstructure, composition, or integrity of end-point repaired shell after 10 weeks, as measured by µCT and SEM imaging, energy-dispersive X-ray (EDX) analysis, and mechanical testing. However, significant interactions between pCO2, the length of exposure to treatment conditions, the strength and inorganic content of shell, and the physiological condition of mussels within OA treatments were observed. These results suggest that while OA does not prevent adult mussels from repairing or mineralizing shell, both OA and shell damage may elicit stress responses that impose energetic constraints on mussel physiology.

show abstract

Section: Sem and µCt Imagingmentioning

confidence: 99%

Mussels Repair Shell Damage despite Limitations Imposed by Ocean Acidification

George

O’Donnell

Concodello

et al. 2022

JMSE

View full text Add to dashboard Cite

show abstract

“…3D image reconstruction was performed in NRecon (Micro Photonics Inc, Allentown, PA), with further rendering in Drishti [65]. The density of repaired shell was estimated by applying a 1 mm diameter cylinder centered on the drill hole of each shell and recording the mean and maximum grayscale values of the scan slices in aggregate.…”

Section: Washington State: Laboratory Ocean Acidification Experimentsmentioning

confidence: 99%

Mussels repair shell damage despite limitations imposed by ocean acidification

George¹,

O’Donnell²,

concodello³

et al. 2022

Preprint

View full text Add to dashboard Cite

Bivalves frequently withstand shell boring attempts by predatory gastropods that result in shell damage that must be quickly repaired to ensure survival. While the processes that underlie larval shell development have been extensively studied within the context of ocean acidification (OA), it remains unclear whether shell repair is impaired by elevated pCO2. To better understand the stereotypical shell repair process, we monitored mussels (Mytilus edulis) with sublethal shell damage within both field and laboratory conditions to characterize the deposition rate, mineral composition, and structural integrity of repaired shell. These results were then compared with a laboratory experiment wherein mussels (Mytilus trossulus) repaired shell damage in one of seven pCO2 treatments (400–2500 µatm). Shell repair proceeded through four distinct stages; shell damage was first covered with an organic film, then mineralized over the course of weeks, acquiring the appearance of nacre after 8 weeks. OA did not impact the ability of mussels to close drill holes, nor the strength or density of the repaired shell after 10-weeks, as measured through mechanical testing and µCT analysis. However, as mussels progressed through each repair stage, significant interactions between pCO2, the length of exposure to treatment conditions, and the strength, inorganic content, and physiological condition of mussels within OA treatments were observed. These results suggest that, while OA may not prevent mussels from repairing shell damage, sustained exposure to elevated pCO2 may induce physiological stress responses that impose energetic constraints on the shell repair process.

show abstract

“…Nowadays, 3D scientific visualization, becomes a common solution for many different purposes [1][2][3][4] and one of the most useful tools for research investigations, revealing hidden information behind the data [5][6][7][8] . For the last two decades, researchers in the 3D scientific visualization field have been experimenting with new ways to more accurately visualize medical and scientific data-sets 3,[9][10][11][12][13][14][15][16][17] . In the current workflow of 3D scientific visualization process, 3D rendered results can be generated using combinations of image processing, segmentation, and rendering techniques [18][19][20] .…”

mentioning

confidence: 99%

A spark of 3D revisualization: new method for re-exploring segmented data

Limaye

Lü

2020

Preprint

Self Cite

View full text Add to dashboard Cite

3D scientific visualization is a popular non-destructive investigation tool, however current imaging processing and 3D visualization software has compatibility barriers which make replicability and reproducibility in research difficult. To solve this, we developed a new revisualization method and demonstrated four case studies using three mainstream image processing and 3D visualization software. Our method offers interchangeability amongst current image processing and 3D visualization software.

show abstract

A new tool for 3D segmentation of computed tomography data:Drishti Paintand its applications

Cited by 3 publications

References 28 publications

Mussels Repair Shell Damage despite Limitations Imposed by Ocean Acidification

Mussels Repair Shell Damage despite Limitations Imposed by Ocean Acidification

Mussels repair shell damage despite limitations imposed by ocean acidification

A spark of 3D revisualization: new method for re-exploring segmented data

Contact Info

Product

Resources

About