click open data this set of slides shows how to generate 3d renderings in avisio from tomographic...
TRANSCRIPT
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Click open data
This set of slides shows how to generate 3D renderings in Avisio from Tomographic Reconstructions from Inspect 3D or ETomo
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Step 2 Select Reconstruction file from Inspect 3D session
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Step 3 A Left click on Loaded Data in project view to display favorite optionsB Right Click to display all available options
1.Click here
Favorite options are displayed after left click
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Step 4. A Click Interactive Thresholding B. The following screen now comes up:
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4C Now adjust thresholding so you can see your nanofibers, blue color indicates the selected area
Slide threshold so you Can see fibers
Change slice number here
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Step 4, Thresholding final step C: Hit Apply to generate thresholded data:
4C: Hit Apply!
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The steps in project view have been dragged to show the workflow that we just did on the data!
Drag colorbars So you can seeall objects of the project
Thresholded data is now generated hiding in new green colorbar
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Step 5: To see the thresholded volume in 3D:A) Get rid of slicing plane by deactivating Interactive ThresholdingB) Select new green box with thresholded data
A) Press Red button to stop displaying threshold plane
B) Left click, then right click
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Step 5 C) Select Volume Rendering, a new yellow double box comes up (it is already connected with an arrow to the thresholded data)D) Use Hand Tool to rotate data freely around in the viewer window
C) New colorbar for Volume rendering
D) Hand Tool
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Generate SurfaceA)Select Thresholded dataB)Select Generate Surface ModuleC)Hit ApplyD)Wait (1-3 minutes)
A) Left Click
B) New module
D) New surface data
Still displaying thresholded data
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Surface Simplification is required because the generated surface is too bigA)Select surface data (lowest green colorbar)B)Open simplification editorC)Set number of faces to 1,800,000 (add two zeros)D)Hit Simplify NowE)Wait some minutes
A) Left Click
Simplification Editor (second from left)
Initial number of faces
Change number of faces
Hit Simplify now
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View SurfaceA) Deselect Volume RenderingB) Right click on the surface module and select Surface View
B) Deselect (color changes from orange to grey)
B) New module surface View
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Auto SkeletonAfter step 4 (creation of the thresholded data), skeletonizing can be done. The Auto Skeleton function however, usually does not work the way we want it.
Left click, right click, type “skeleton” in the search field and select when it shows up
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Hit Apply on the green button
A red colorbar “Auto Skeleton” will appear, left click to select it
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Manual SkeletonSeveral Individual steps need to be performed depending on the dataset:resampling, closing, dilating, eroding. But there is no standard way and some trial and error.After applying those steps/filters/functions, the thinning function must be used and only if it yields a graph/line – like skeleton the Auto Skeleton function will result in the desired skeleton and statistical data can be generated
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Fill in Steps on Surface rendering. Every time I run a surface rendering in Avizio it crashes.
Reduce data set first?
Best way to do that?
Then how to edit surface plot properties ….
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Different data types
File ending Contains Description Typical sizeTilt series .mrc
.stHeader and tilted images One image per angle,
angles and general informationare stored in header
2Mb per image (1024x1024x2byte) 280 Mb for 140 angles
reconstruction .rec Aligned images Grid (voxels) containing parallel images (pixels) (such as slice and view)
2 bytes per voxel 400nm thick 1.1 Gb
Avizo modified .filteredetc
Voxels with intensity Grid generated by Avizo after specific function is applied
Same as reconstruction or reduced (e.g. when resampled to certain size)
Avizo segmentation .label Voxels (binary) grouped by objects of interest
Voxels assigned to segmentsIntensity segment#
Same as reconstruction
Avizo surface .surface Mesh of Vertices and faces created from grid using specific algorithm
Ca. 10 Mb, fast computer can handle 100Mb
Other surface .ply.stl
Mesh of vertices and faces Created from vertices in space
Ca. 10 Mb, fast computer can handle 100Mb
Avizo skeleton and other measurements
.SptGraphetc
Skeleton: Lines and nodes,Charts, histograms, etc
Skeleton contains of lines and connection of the lines (nodes) modeling thin features,Measurements are numbers in text format and plotted accordingly
Very small < 1Mb
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Tilt series
Volume Rendering
Label Field
Surface
Surface
Video
Data acquisition
Numbers
Reconstruction
Reconstruction file
Inspection
Segmentati
on
Surface reconstruction
Simplification
Animation
Skeletonizing
Spatial Graph
Measurements