working with avizo basics: loading the software: converting 3d

Avizo training materials, BRC-Imaging Facility, TJP Jan. 2015

Working With Avizo

Basics:

Avizo is an image analysis software package designed to work smoothly with 3D images—

whether data from confocal or CT, or 3D rendered images.

The BRC imaging core has an Avizo site license that allows the software to be run on at least

two computers simultaneously. Please quit the software when you are not using it, so that

other researchers can have access to it.

Loading the software:

Go to the shared BRC-Imaging folder. Copy the file named “Avizo-8.1.1-Windows-Visual2010-

64” in the folder \ALL USER IMAGES HERE_2015\VIZ\Avizo to your computer.

Start the program, choose a folder to download to, read the user agreement, etc. You can

choose whether to load Avizo Standard, Avizo Fire, or both. Choose “Use FNP Server/Floating

Licenses” when asked about the software license.

Once the software download is complete, start up the software. The main FNP server is

keyserver2.biotech.cornell.edu—click “test” to confirm the correct address . Click Activate. An

error message will come up—this appears to be a software glitch. Click Cancel, shut down the

software, and restart. Avizo should now start up normally with the correct FNP license.

Converting 3D data into a 3D print:

Open Avizo Standard and open your data. If opening a set of 2D image slices, you may need to

define the distance between slices.


Select a display to show the data by right-clicking on the object (the green icon in the Project

View window labeled with your filename) and going to the Display folder, or choose one of the

buttons at the top of the Project View window that appear when left-clicking an object.

Some possible imaging choices:

Ortho view: slices through the x, y, and z planes

ROI box: shows the edges of the available data

Volume Rendering: shows grayscale image of complete data set.


Volume rendering of dataset after adjusting colormap and alpha scale. This is done by clicking

the “volume Rendering” object and making adjustments in the Properties window in the lower

right side.

Right click on object with the object filename, go to Image Segmentation, and Edit Label Field.

You will now be in a separate tab in the main panel for your data set:

Edit Label Field tab and data imaging window

To select the area you wish to print:

Click on the magic wand (highlighted in the screen capture above), click in the region you want

to select, and adjust the overall volume using the sliders. The area you select should be grayed


out and more easily visible. You may want to choose “All Slices” to extend your selection

through the full volume of the sample, and you may want to choose “Same Material Only” to

remove irrelevant sections of the data (the blanket in the above image, for example). When you

have selected the area of interest, add it to a data label by clicking on the label field (Exterior

and Inside are shown above), then clicking on the

symbol. Multiple regions can be selected and made part of the same label (in the example

above, the denser nose and eyes were separately selected and added to the label “Inside”.

For a multiple color print, select the separate regions and give them different labels. These

different labels will need to be saved as separate files and added together later in the Makerbot

software.

When the regions have been selected, go back to the Project View Tab. Create a new display for

the “filename.labels” object or move the connecting line from the original file to the labels file,

as seen below:

Right click on the “filename.labels” X: under “Compute”, select “Generate Surface”. Click

“Create”.


Make any desired adjustments and click Apply:

This will generate a new X called “filename.surf”. Display this data set as a surface view to show

a smoothed-out version of the data above:


Adjustments can be made by clicking on the “Generate Surface” tab, making modifications, and

clicking Apply.

The very image shown here is a somewhat large file which may take a long time for the

Makerbot to analyze when it’s time to print. The file size can be reduced by simplifying the

data. To simplify the data, click on the “simplification editor” button highlighted in the screen

shot above. (This menu is reached by clicking the “filename.surf” X.) Make any desired

adjustments and click “Simplify now”.

The number of points listed should be greatly reduced, and the object will look somewhat more

polygonal, though still less pixelated than in the “filename.labels” object.

Click on the “filename.surf” object and save the data. Makerbot can use the .stl file format.


The file is now ready to be processed with the Makerbot software.

For assistance with setting up the Makerbot and Makerbot software, contact BRC-Imaging staff.

Data analysis:

Open your data or data set, and adjust scaling factors if requested by the software. Right click

on the object in the Project View tab and make a selection in the Display folder to show the

data set. The most commonly used examples include:

Ortho view: slices through the x, y, and z planes

ROI box: shows the edges of the available data

Volume Rendering: shows grayscale image of complete data set.

Ortho, ROI, and Volume Rendering Views all displayed concurrently.

To select particles of a particular brightness within the image, right click on the main file object

Image Segmentation->Interactive Thresholding


Image Thresholding menu in the Properties window

Adjusting the Colormap slider will adjust the brightness of the image, adjusting the Threshold

slider will change the data selected (shown here in blue.) Adjusting the Preview Slice Number

slider will show different slices through the viewing area. When the thresholding is set the way

you want it, click Apply. The object “filename.thresholded” will display the binary dataset. Note

on the image below that some of the particles are touching. We’ll address this next, but if your

data is exactly the way you want it, you can skip to the labeling.

To separate, right click on the “filename.thresholded” object Image Processing Separating

and FillingSeparate Objects


Before hitting Apply, confirm that Interpretation is set to 3D, so that later analysis looks at the

entire volume of the individual particles. Other factors can be played with by changing and

hitting Apply; the resulting analysis will change but it will not create more objects in the project

view. “filename.separate” will be created.

The same thresholded slice before (left) and after (center) a successful segmentation. A poor

segmentation is shown on the right—note that some “correct” segmentation locations are

missing, and some “incorrect” locations are segmented. The “marker extent” setting was

changed between these two segmentations.

Right-click on “filename.separate” Image Segmentation Labeling

In the Properties tab, Interpretation should be 3D. After clicking Apply, an object named

“filename.labels” will show up in the project view. Connect the Ortho Slice to this object to see

the labels.


Each grain is represented as a separate color.

A few further filters you may want to use before analyzing your data:

Image SegmentationRemove Small Spots: removes all features smaller than a number of

voxels defined by the user.

Image Processing Features Selection Border Kill removes particles on the edge of an image

(not the edge of the surface: note that for the example above, the edges form a box around the

cylindrical sample, and the Border Kill function removes particles touching the box edge.


Image SegmentationMulti-Thresholding: creates multiple segmentations based on

brightness. Useful for separating materials of varying densities in analysis.

To analyze labeled data:

Right click the “filename.labels” object (or post-processing object)Measure and

AnalyzeIndividual MeasuresLabel Analysis. Clicking the “…” button next to “Measures”

gives a menu with many options, but the “basic” choice in the drop down menu includes some

standard measurements such as volume and location. An object named “filename.Label-

Analysis” will be created. Click on the object and click Show to bring up a table that includes all

of the data and some basic statistical analysis.

Clicking on the crosshairs above the table and selecting an entry will show you the location of

that particle.

Further filtering can be done by right-clicking “filename.Label-Analysis Measure and

AnalyzeAnalysis Filter. Hitting Apply will automatically update the Table window with a new

tab labeled “filename.Analysis-Filter” that includes any unfiltered data and the corresponding

statistics on the filtered population.


Removing particles with a volume larger than 200000, which are composed of unsegmented

beads at the edges of the cylinder.

The data can be exported at this time.


Making a Movie:

(I would recommend using Osirix or Volocity for this unless you specifically want to visualize

data that has been analyzed; even the demo examples given by Aviso are not as nice as can be

quickly made on either of these programs.)

Open your data, and display it by right clicking on the object in the Project View window and

choosing the desired setting under Display.

Right click on “filename” object in the Project View Animate Transform Sequence.

In this menu, you can rotate or zoom in on the data and save individual “save points”

Right click on the sequenceComputeMovie Maker to take the sequence and transform it

into a movie.

working with avizo basics: loading the software: converting 3d

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