Click open data

This set of slides shows how to generate 3D renderings in Avisio from Tomographic Reconstructions from Inspect 3D or ETomo

Step 2 Select Reconstruction file from Inspect 3D session

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

Step 4. A Click Interactive Thresholding B. The following screen now comes up:

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

Step 4, Thresholding final step C: Hit Apply to generate thresholded data:

4C: Hit Apply!

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

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

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

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

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

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

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

Hit Apply on the green button

A red colorbar “Auto Skeleton” will appear, left click to select it

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

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 ….

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

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