资源描述
Click to edit Master title style,Click to edit Master text styles,Second level,Third level,Fourth level,Fifth level,*,Visualization Tool,for,Flow Cytometry Data Standards Project,Evgeny Maksakov,CS533C,Department of Computer Science,UBC,in collaboration with,Terry Fox Laboratory,BC Cancer Agency,(Prof.Ryan Brinkman&Dr.Josef Spidlen),1,Today,Flow Cytometry Overview,Dataset description,Existing Visualizations Overview,Data analysis,Current(FlowJo),Proposed,Prototype Progress,Future Work,2,Flow,Cyto,metry,Measure,Cell,Measuring properties of cells in a fluid stream,3,List of Flow Cytometry Application Fields,Chromatin structure,Total protein,Lipids,Surface charge,Membrane fusion/runover,Enzyme activity,Oxidative metabolism,Sulfhydryl groups/glutathione,DNA synthesis,DNA degradation,Gene expression,Immunophenotyping,DNA cell cycle/tumor ploidy,Membrane potential,Ion flux,Cell viability,Intracellular protein staining,pH changes,Cell tracking and proliferation,Sorting,Redox state,The list is taken from,4,Flow Cytometry(FCM),5,Dataset Properties,Typically for research at the TFL:,100,000+events,5-10 dimensions,Capability:,1,000,000 events(cells going through the laser beam)per dataset,Up to 20 dimensions,6,Dimensions(2 basic dimensions),(Size),(Laser),(Granularity),7,Dimensions(GFP intensity&PI),Pictures is taken from :/en.wikipedia.org/wiki/Image:Aequorea_victoria.jpg&,Green Fluorescent Protein intensity,measures gene expression,Mice glow green under ultraviolet light,PI(Propidium Iodide)dye intensity,measures cells viability(life cells expunge the dye),Aequorea Victoria(natural owner of GFP),8,Dimensions(16 fluorescence intensities),Picture from:,9,Attaching markers to cells,10,Current Visualization Solutions,Made deliberately for FCM:,FlowJo,(scatterplots,histograms,contour diagrams),FACSDiva,(scatterplots,histograms,contour diagrams),11,Current Visualization Solutions,Universal data visualization tool:,GGobi,Draw dotplots and scatterplots,barcharts,spineplots and histograms,parallel coordinate plots,scatterplot matrices,Link data points and lines between plots using brushing and identification,Pan and zoom,Rotate data in 3D and tour high-dimensional data using sequences of 1D,2D and 2x1D projections,Uses R language for data manipulation,12,Data Analysis Process(FlowJo),Event Count,is a total number of cells passed through the laser beam,Negative control,Gates,(each scatterplot is a new window),Important note:,sequence of actions is the same all the time for negative control!,13,Data Analysis Process(FlowJo),Looking for result,Marked cells(result),Non-marked cells,Important note:,Same gates as in neg.control apply automatically on the positive set!,14,Other forms of result visualization(FlowJo),15,Proposal,User requirements(based on user studies):,See all dimensions at once,Improve analysis sequence,Leave scatterplots and histograms(scientists used to them),Gating/Filtering feature,Provide better usability than FlowJo,Solutions:,Use Parallel Coordinates with Gating/Filtering,Implement data clustering throughout dimensions,Include scatterplots and histograms in the interface,Make effective,convenient and interactive interface,16,Interface for FCM Data Analysis,17,Prototype progress,Highlighting of the gate.Random set,3000 points,7 dimensions.,18,Prototype progress,Filtering.Random set,100 000 points,7 dimensions.Full scale rendering takes 1min.,19,Prototype progress,Interaction results.Random set,3000 points,7 dimensions.,20,Future Work,Visualization of the real data,Clustering,Optimization,User evaluation,21,3D Parallel Coordinate System for FCM,Marc Streit,at al.(2006),22,3D Parallel Coordinate System for FCM,Picture from Marc Streit at al.(2006),-Does not provide any new information about dataset,Introduces visual occlusions,Have to rotate to see all data,Unavailable,23,Questions,24,
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