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
stop displaying thre
plane
B) Left click, t
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 f
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 modul
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)
A) Left Click
D) Hit Simplify Now
E) Wait some minutes
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 ….
Different data types
File ending
Contains
Description
Typical size
Tilt series
.mrc
.st
Header 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
.filtered
etc
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
segments
Intensity  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
.SptGraph
etc
Skeleton: Lines and nodes,
Charts, histograms, etc
Skeleton contains of
lines and connection of
Very small < 1Mb
Data
acqui
sition
Tilt series
Reco
nstru
ction
Surface
reconst
ruction
Skeleto
nizing
Measur
ements
Reconstruction
file
Surface
Spatial Graph
Numbers
Inspe
ction
Simplifi
cation
Volume
Rendering
Surface
Segm
entati
on
Label Field
Animati
on
Video