STUCK AT SEA: Using Imaris software to visualize in 3-D ......STUCK AT SEA: Using Imaris software to...
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STUCK AT SEA: Using Imaris software to visualize in 3-D barnacle and oyster confocal data Caroline Zhang 1 , Dr. Andrew S. Mount 2 , Dr. Vera Chan 2 , Dr. Vetria Byrd 2 1 Emory University 2 Clemson University REU Site: Research Experience for Undergraduates in Collaborative Data Visualization Applications • June 1 – July 24, 2015 • Clemson University • Clemson, South Carolina • REU Funded by NSF ACI Award 1359223 • XSEDE ‘15 travel sponsored by NSF Supplemental OSP Award #20130251 1-004 Abstract Results and Discussion Methods Conclusion The mechanism that barnacle cyprids use to attach onto surfaces (Gohad et. al. 2014; Aldred et. al. 2013) and the process that oysters use for shell mineralization are currently being studied. (Mount et. al. 2004) Previous research has used confocal microscopy and computer software to determine the respective components and mechanisms of each organism, however these results have been limited because they do not allow enough data analysis. This project used the same confocal data and Imaris software to improve upon the previous 3-D visualizations of these areas by enhancing the different structures to allow for more insightful data analysis. Researchers have been able to use the visualizations to discover key information about the location and production of chitin, a polysaccharide polymer found in insect exoskeletons, thought to be a major component of barnacle adhesive; and have been able to analyze the presence of matrix metalloproteinases (MMPs), an enzyme related to wound reparation, theorized to be involved in shell mineralization in oysters. The use of improved visualization tools, such as Imaris, will be a significant factor in future study methodologies related to these research areas, as well as other studies involving confocal data analysis. Acknowledgements Raw confocal data acquired. Input into Imaris software and irrelevant data channels filtered out. Specific areas of interest represented with structures to highlight their distinctive features by using Imaris tools such as “surfaces” and “spots”. Movie clips demonstrating the different visualization techniques generated. Data refined as advised by research mentors. The advanced visualization of barnacle and oyster data resulted in the use of Imaris for confocal microscopy data sets. It has been useful in highlighting specific features of the data for analysis that is otherwise indistinguishable. The use of this visualization technique will allow for more insightful data analysis on future projects in Dr. Mount’s group with similar data types. Figure 2. (A) Left, original oyster hemocyte cell data. Right, surfaces added for cell membranes (red) and nuclei (blue) to define borders. Spots added for chitin (green). Visualization enhances the relationship of the relative positions of the structures and provides insight of possible chitin production locations in the cells. (B) Left, original oyster hemocyte data. Right, irrelevant data channels removed and surfaces added to nuclei (blue) and spots added to degraded collagen (green) to better show collagen intensity. Provides greater insight to the components of the oyster shell mineralization mechanism. (C) Left, original hemocyte data. Right, irrelevant data channels removed and surfaces added to the nuclei (blue) to distinguish between each structure and aid counting. Figure 1: (A) Left, original barnacle cyprid data. Right, surfaces and spots added to emphasize the production and location of chitin (green). Enhances knowledge of chitin aggregation in barnacle cyprids and the surface characteristics of the chitin plaques. (B) Left, original barnacle cyprid data. Right, surfaces added to the cell membrane (pink) and chitin (green). Acute biological relevance as it lead to discovery of the membrane surrounding most of the chitin plaque, provides insight on chitin production mechanism in cyprids. References 1. Gohad N, Aldred N, Hartshorn C, Jong Lee Y, Cicerone M, Orihuela B, Clare A, Rittschof D, Mount A. Synergistic roles for lipids and proteins in the permanent adhesive of barnacle larvae. Nature Communications. 2014 [accessed 2015 Jul 21];5. 2. Aldred N, Gohad N, Petrone L, Orihuela B, Liedberg B, Ederth T, Mount A, Rittschof D, Clare A. Confocal microscopy-based goniometry of barnacle cyprid permanent adhesive. Journal of Experimental Biology. 2013 [accessed 2015 Jul 21];216(11):1969- 1972. 3. Mount A, Wheeler A, Paradkar R, Snider D. Hemocyte-Mediated Shell Mineralization in the Eastern Oyster. Science. 2004 [accessed 2015 Jul 21];304(5668):297-300. C B A B A
Transcript of STUCK AT SEA: Using Imaris software to visualize in 3-D ......STUCK AT SEA: Using Imaris software to...
STUCK AT SEA: Using Imaris software to visualize in 3-D barnacle and oyster confocal data
Caroline Zhang1, Dr. Andrew S. Mount2, Dr. Vera Chan2, Dr. Vetria Byrd2
1Emory University 2Clemson University
REU Site: Research Experience for Undergraduates in Collaborative Data Visualization Applications • June 1 – July 24, 2015 • Clemson University • Clemson, South Carolina
• REU Funded by NSF ACI Award 1359223• XSEDE ‘15 travel sponsored by
NSF Supplemental OSP Award #20130251 1-004
Abstract Results and Discussion
Methods
ConclusionThe mechanism that barnacle cyprids use to attach ontosurfaces (Gohad et. al. 2014; Aldred et. al. 2013) and theprocess that oysters use for shell mineralization arecurrently being studied. (Mount et. al. 2004) Previousresearch has used confocal microscopy and computersoftware to determine the respective components andmechanisms of each organism, however these resultshave been limited because they do not allow enough dataanalysis. This project used the same confocal data andImaris software to improve upon the previous 3-Dvisualizations of these areas by enhancing the differentstructures to allow for more insightful data analysis.Researchers have been able to use the visualizations todiscover key information about the location andproduction of chitin, a polysaccharide polymer found ininsect exoskeletons, thought to be a major component ofbarnacle adhesive; and have been able to analyze thepresence of matrix metalloproteinases (MMPs), anenzyme related to wound reparation, theorized to beinvolved in shell mineralization in oysters. The use ofimproved visualization tools, such as Imaris, will be asignificant factor in future study methodologies related tothese research areas, as well as other studies involvingconfocal data analysis.
Acknowledgements
Raw confocal data acquired. Inputinto Imaris software and irrelevantdata channels filtered out.
Specific areas of interestrepresented with structures tohighlight their distinctive featuresby using Imaris tools such as“surfaces” and “spots”.
Movie clips demonstrating thedifferent visualization techniquesgenerated. Data refined as advisedby research mentors.
The advanced visualization ofbarnacle and oyster data resultedin the use of Imaris for confocalmicroscopy data sets. It hasbeen useful in highlightingspecific features of the data foranalysis that is otherwiseindistinguishable. The use ofthis visualization technique willallow for more insightful dataanalysis on future projects in Dr.Mount’s group with similar datatypes.
Figure 2. (A) Left, original oyster hemocyte cell data. Right, surfaces added for cell membranes (red) andnuclei (blue) to define borders. Spots added for chitin (green). Visualization enhances the relationship of therelative positions of the structures and provides insight of possible chitin production locations in the cells. (B)Left, original oyster hemocyte data. Right, irrelevant data channels removed and surfaces added to nuclei(blue) and spots added to degraded collagen (green) to better show collagen intensity. Provides greater insightto the components of the oyster shell mineralization mechanism. (C) Left, original hemocyte data. Right,irrelevant data channels removed and surfaces added to the nuclei (blue) to distinguish between each structureand aid counting.
Figure 1: (A) Left, original barnacle cyprid data. Right, surfaces and spots added to emphasize the productionand location of chitin (green). Enhances knowledge of chitin aggregation in barnacle cyprids and the surfacecharacteristics of the chitin plaques. (B) Left, original barnacle cyprid data. Right, surfaces added to the cellmembrane (pink) and chitin (green). Acute biological relevance as it lead to discovery of the membranesurrounding most of the chitin plaque, provides insight on chitin production mechanism in cyprids.
References1. Gohad N, Aldred N, Hartshorn C, Jong Lee Y,
Cicerone M, Orihuela B, Clare A, RittschofD, Mount A. Synergistic roles for lipids and proteins in the permanent adhesive of barnacle larvae. Nature Communications. 2014 [accessed 2015 Jul 21];5.
2. Aldred N, Gohad N, Petrone L, Orihuela B, Liedberg B, Ederth T, Mount A, RittschofD, Clare A. Confocal microscopy-based goniometry of barnacle cyprid permanent adhesive. Journal of Experimental Biology. 2013 [accessed 2015 Jul 21];216(11):1969-1972.
3. Mount A, Wheeler A, Paradkar R, Snider D. Hemocyte-Mediated Shell Mineralization in the Eastern Oyster. Science. 2004 [accessed 2015 Jul 21];304(5668):297-300.
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