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AMI 2015 Vesalian Scholar Thesis Presentation

Mariya Khan
Mariya Khan

A summary of the workflow investigation for collaborative concept development by medical animators and biomedical research experts, undertakes as part of a masters thesis project at Johns Hopkins University School of Medicine Art as Applied to Medicine Program.

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Actomyosin Network in Mechanosensation and Cytokinesis A Novel Animation Workflow Mariya Khan Johns Hopkins University School of Medicine Department of Art as Applied to Medicine Douglas N. Robinson, Ph.D., Departments of Cell Biology, Pharmacology and Molecular Sciences, and Chemical and Biomolecular Engineering Johns Hopkins University School of Medicine
Introduction Cellular Mechanosensing What is it? Cells chemical response to mechanical stresses from the environment Cytoskeleton reorganization in cell motility and cytokinesis Cytoskeleton Actin meshwork Cross-linker proteins Myosin II (contractile) Cytoskeleton in animal cells: actin filaments (red), microtubules (green), nucleus (blue). http://bscb.org/learning-resources/softcell-e-learning/cytoskeleton-the-movers-and- shapers-in-the-cell/
Cellular Mechanosensing in Health Physiological function Blood pressure regulation Tissue homeostasis Bone remodeling Muscle growth Senses of hearing, touch, proprioception Disease Hypertension Cancer Proliferation Migration Differentiation Chronic Obstructive Pulmonary Disease Degenerative Motor Neuron Disease (most likely ) Introduction
Thesis Goals Develop workflow Efficient storyboarding Optimal software Develop animatic: Explain topics: Actomyosin function Feedback loops in the cell Audience: High school, college students Scientists Policy makers and funders Develop data-driven animation method in Cinema 4D Introduction Cytoskeleton in Dictyostelium cells: myosin II (green), tubulin (red). Douglas Robinson, Departments of Cell Biology, Pharmacology and Molecular Sciences, Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine
Workflow Development Combined animatic and storyboard Adapted video postproduction workflow Optimal software and best practices Script embedding Speech analysis Materials and Methods: Workflow Development
Materials and Methods: Workflow Development Animatic creation Storyboard export Custom actions Adobe Photoshop Timelinepanel AnimDessin2plugin Renamyplugin Adobe Audition Narration audio recording Audio editing AnimDessin2 plugin and Adobe Photoshop timeline panel
Adobe Premiere Embedded script preserved Speech analysis in CC 7.2.2 Master sequence Adobe Story Materials and Methods: Workflow Development Script writing and scene organization Free version for collaboration Adobe Prelude Adobe Story script embedding Custom metadata template creation Adobe Story interface Adobe Story panel in Adobe Prelude interface
Adobe After Effects Materials and Methods: Workflow Development Live link to Adobe Premiere Best practices Project organization/markers Live link to Cinema 4D with CINEWARE
Materials and Methods: Data-driven animation in Cinema 4D Data-driven animation in Cinema 4D Rotoscoping: unique application of Metaballs
Materials and Methods: Data-driven animation in Cinema 4D Data-driven animation in Cinema 4D ASCII Point Cloud Data Import Improved Xpresso setup for graph generation
Materials and Methods: Data-driven animation in Cinema 4D X-Particles System ASCII Animated Data Import Concentration data for furrow Myosin II copied into Emitter Density property Data-driven animation in Cinema 4D
Materials and Methods: Data-driven animation in Cinema 4D
Results Improved workflow Data-driven animation in Cinema 4D Animatic The results of this thesis will be available for viewing at: www.mariyakhan.com robinsonlab.cellbio.jhmi.edu Results Myosin II Bipolar Thick Filament assembly sequence screenshot Myosin II Actin interaction sequence screenshot
Results Actomyosin Network in Mechanosensation and Cytokinesis Thesis Animatic, March 2015
Discussion Future Developments Fully rendered animation Animation within interactive web application Workflow Developments Metadata, scene presets, automation Discussion
Acknowledgements The Vesalius Trust Douglas N. Robinson, Ph.D., Professor, Departments of Cell Biology, Pharmacology and Molecular Sciences, and Chemical and Biomolecular Engineering at Johns Hopkins University School of Medicine, and preceptor for this project. Corinne Sandone, M.A., C.M.I., F.A.M.I., Director, Associate Professor, Department of Art as Applied to Medicine in the Johns Hopkins University School of Medicine, and my departmental advisor. Sarah L. Poynton, Ph.D., David Rini, Sandra Gabelli, Anne Altemus, Donny Bliss, Thomas Brown, Graham Johnson Jennifer E. Fairman, Juan Garcia, Dacia Balch, Gary Lees, Ian Suk, Norman Baker, Tim Phelps, Elaine Gerstenfeld, Virginia Ferrante Classes of 2015, 2014 and 2016 My family
THANK YOU

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AMI 2015 Vesalian Scholar Thesis Presentation

  • 1. Actomyosin Network in Mechanosensation and Cytokinesis A Novel Animation Workflow Mariya Khan Johns Hopkins University School of Medicine Department of Art as Applied to Medicine Douglas N. Robinson, Ph.D., Departments of Cell Biology, Pharmacology and Molecular Sciences, and Chemical and Biomolecular Engineering Johns Hopkins University School of Medicine
  • 2. Introduction Cellular Mechanosensing What is it? Cells chemical response to mechanical stresses from the environment Cytoskeleton reorganization in cell motility and cytokinesis Cytoskeleton Actin meshwork Cross-linker proteins Myosin II (contractile) Cytoskeleton in animal cells: actin filaments (red), microtubules (green), nucleus (blue). http://bscb.org/learning-resources/softcell-e-learning/cytoskeleton-the-movers-and- shapers-in-the-cell/
  • 3. Cellular Mechanosensing in Health Physiological function Blood pressure regulation Tissue homeostasis Bone remodeling Muscle growth Senses of hearing, touch, proprioception Disease Hypertension Cancer Proliferation Migration Differentiation Chronic Obstructive Pulmonary Disease Degenerative Motor Neuron Disease (most likely ) Introduction
  • 4. Thesis Goals Develop workflow Efficient storyboarding Optimal software Develop animatic: Explain topics: Actomyosin function Feedback loops in the cell Audience: High school, college students Scientists Policy makers and funders Develop data-driven animation method in Cinema 4D Introduction Cytoskeleton in Dictyostelium cells: myosin II (green), tubulin (red). Douglas Robinson, Departments of Cell Biology, Pharmacology and Molecular Sciences, Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine
  • 5. Workflow Development Combined animatic and storyboard Adapted video postproduction workflow Optimal software and best practices Script embedding Speech analysis Materials and Methods: Workflow Development
  • 6. Materials and Methods: Workflow Development Animatic creation Storyboard export Custom actions Adobe Photoshop Timelinepanel AnimDessin2plugin Renamyplugin Adobe Audition Narration audio recording Audio editing AnimDessin2 plugin and Adobe Photoshop timeline panel
  • 7. Adobe Premiere Embedded script preserved Speech analysis in CC 7.2.2 Master sequence Adobe Story Materials and Methods: Workflow Development Script writing and scene organization Free version for collaboration Adobe Prelude Adobe Story script embedding Custom metadata template creation Adobe Story interface Adobe Story panel in Adobe Prelude interface
  • 8. Adobe After Effects Materials and Methods: Workflow Development Live link to Adobe Premiere Best practices Project organization/markers Live link to Cinema 4D with CINEWARE
  • 9. Materials and Methods: Data-driven animation in Cinema 4D Data-driven animation in Cinema 4D Rotoscoping: unique application of Metaballs
  • 10. Materials and Methods: Data-driven animation in Cinema 4D Data-driven animation in Cinema 4D ASCII Point Cloud Data Import Improved Xpresso setup for graph generation
  • 11. Materials and Methods: Data-driven animation in Cinema 4D X-Particles System ASCII Animated Data Import Concentration data for furrow Myosin II copied into Emitter Density property Data-driven animation in Cinema 4D
  • 12. Materials and Methods: Data-driven animation in Cinema 4D
  • 13. Results Improved workflow Data-driven animation in Cinema 4D Animatic The results of this thesis will be available for viewing at: www.mariyakhan.com robinsonlab.cellbio.jhmi.edu Results Myosin II Bipolar Thick Filament assembly sequence screenshot Myosin II Actin interaction sequence screenshot
  • 14. Results Actomyosin Network in Mechanosensation and Cytokinesis Thesis Animatic, March 2015
  • 15. Discussion Future Developments Fully rendered animation Animation within interactive web application Workflow Developments Metadata, scene presets, automation Discussion
  • 16. Acknowledgements The Vesalius Trust Douglas N. Robinson, Ph.D., Professor, Departments of Cell Biology, Pharmacology and Molecular Sciences, and Chemical and Biomolecular Engineering at Johns Hopkins University School of Medicine, and preceptor for this project. Corinne Sandone, M.A., C.M.I., F.A.M.I., Director, Associate Professor, Department of Art as Applied to Medicine in the Johns Hopkins University School of Medicine, and my departmental advisor. Sarah L. Poynton, Ph.D., David Rini, Sandra Gabelli, Anne Altemus, Donny Bliss, Thomas Brown, Graham Johnson Jennifer E. Fairman, Juan Garcia, Dacia Balch, Gary Lees, Ian Suk, Norman Baker, Tim Phelps, Elaine Gerstenfeld, Virginia Ferrante Classes of 2015, 2014 and 2016 My family

Editor's Notes

  • #2: Good afternoon, ladies and gentlemen. Today I would like to share with you my thesis developing a novel animation workflow for visualizing the research conducted at the Robinson Lab at Johns Hopkins University School of Medicine Actomyosin Network in Mechanosensation and Cytokinesis
  • #12: Two Emitters and two Groups Furrow Myosin Polar Myosin Initial particle count: 1 million Animated cube representing Furrow Myosin X-Particles Collider tag with Polar Myosin excluded Modifiers: Kill, Cover/Target Concentration data for furrow Myosin II copied into Emitter Density property