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

Step 2 Select Reconstruction file from Inspect 3D session

Step 3 A Left click on Loaded Data in project view to display favorite options B Right Click to display all available options Favorite options are displayed after left click 1.Click here

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 Change slice number here Slide threshold so you Can see fibers

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!

Thresholded data is now generated hiding in new green colorbar Drag colorbars So you can see all objects of the project

Step 5: To see the thresholded volume in 3D: A) Get rid of slicing plane by deactivating Interactive Thresholding B) 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 D) Hand Tool C) New colorbar for Volume rendering

Generate Surface A) Select Thresholded data B) Select Generate Surface Module C) Hit Apply D) Wait (1-3 minutes) A) Left Click B) New module Still displaying thresholded data D) New surface data

Surface Simplification is required because the generated surface is too big A) Select surface data (lowest green colorbar) B) Open simplification editor C) Set number of faces to 1,800,000 (add two zeros) D) Hit Simplify Now E) Wait some minutes A) Left Click Simplification Editor (second from left) Initial number of faces Change number of faces Hit Simplify now

View Surface A) Deselect Volume Rendering B) Right click on the surface module and select Surface View B) Deselect (color changes from orange to grey) B) New module surface View

Auto Skeleton

After 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

A red colorbar “Auto Skeleton” will appear, left click to select it Hit Apply on the green button

Manual Skeleton

Several 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 ….

Tilt series reconstruction Avizo modified Avizo segmentation Avizo surface Other surface Avizo skeleton and other measurements

File ending

.mrc

.st

.rec

.filtered

etc .label

.surface

Different data types

Contains

Header and tilted images Aligned images

Description

One image per angle, angles and general informationare stored in header

Typical size

2Mb per image (1024x1024x2byte)  280 Mb for 140 angles Grid (voxels) containing parallel images (pixels) (such as slice and view) 2 bytes per voxel  400nm thick  1.1 Gb Voxels with intensity Grid generated by Avizo after specific function is applied Same as reconstruction or reduced (e.g. when resampled to certain size) Voxels (binary) grouped by objects of interest Mesh of Vertices and faces Voxels assigned to segments Intensity  segment# created from grid using specific algorithm Same as reconstruction Ca. 10 Mb, fast computer can handle 100Mb .ply

.stl

Mesh of vertices and faces Created from vertices in space Ca. 10 Mb, fast computer can handle 100Mb .SptGraph

etc Skeleton: Lines and nodes, Charts, histograms, etc Skeleton contains of lines and connection of the lines (nodes) Very small < 1Mb

Data acqui sition Tilt series Reco nstru ction Reconstruction file Inspe ction Volume Rendering Segm entati on Label Field Surface reconst ruction Surface Simplifi cation Surface Animati on Video Skeleto nizing Spatial Graph Measur ements Numbers