Recipe Description


The 3D Object Analysis recipe in Aivia detects objects (such as cells and nuclei) and generates surface reconstructions of the objects in 3D volumetric images. The recipe provides a count of the number of detected objects as well as morphological and intensity measurements of individual objects.

Parameters and Presets


Parameters

Parameters and their descriptions are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Detection
Average Object Radius (Remove Background only)
0
1,000
Specifies the radius of a typical object in the image for objects enhancement and background removal; a lower value will preserve smaller objects
Detection
Min Edge Intensity
0
255 (8-bit)
65,535 (16-bit)
Specifies the minimum object intensity (found typically at the edge of the object) for detection; when Remove Background is enabled, this parameter value is used to specify the minimum object intensity on the enhanced image; a lower value will detect bigger and more objects
Partition
Object Radius
0
1,000
Specifies the range of objects to be included in the analysis results based on the radius of the detected objects
Partition
Smoothing Factor
0
10
Adjusts the amount of smoothing applied to the surface reconstructions of the detected objects; a lower value will generate surfaces with greater similarity to the input image
Partition
Min Edge-to-Center Distance
(Apply Partition only)
0
1,000
Specifies the minimum distance from the center of an object to the edge that is touching its closest neighboring object; this parameter is enabled only when Apply Partition is enabled; a lower value will apply objects partition more aggressively resulting in smaller, more uniform objects

Presets

There are two preset groups in the recipe: Detection and Partition; each group has three pre-configured parameter grouping to help you get started on the analysis. The default preset values are as follows:

Detection

Parameter Name
Low
Medium
High
Average Object Radius
5
20
100
Min Edge Intensity
10 (8-bit)
2621 (16-bit)
5 (8-bit)
1311 (16-bit)
3 (8-bit)
655 (16-bit)

Partition

Parameter Name
Small
Medium
Large
Object Radius
2 - 5
20 - 50
100 - 300
Smoothing Factor
1
2
5
Min Edge-to-Center Distance
2
20
100

Measurements


The 3D Object Analysis recipe generates morphological and intensity measurements for each detected 3D object as well as a count of the total number of 3D objects on the image. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia. The measurements generated by the recipe are as follows.
  • Morphological
    • Surface Area
    • Volume
    • Convex Hull Volume
    • Volume Ratio
  • Intensity (measured on the input channel)
    • Average
    • Maximum
    • Minimum
    • Total
    • Standard Deviation
  • Summary
    • Object Count

Tutorial


Before beginning the tutorial, please download the 3D Object Analysis Demo image (3DObjAnalysisDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.

  1. Unzip the demo file and load the demo image, 3DObjAnalysisDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the 3D Object Analysis recipe
  3. Click on the Show Advanced Interface icon showAdvOptions.PNG to expand the Recipe Console
  4. Click on the Switch Recipe Operations icon switchableIcon.PNG to show the list of available recipe operations; select the Remove Background option from the dropdown menu
  5. Select the following settings on the recipe:
    • Average Object Radius: 5
    • Min Edge Intensity: 5
    • Object Radius: 2 - 6
    • Smoothing Factor: 2
    • Min Edge-to-Center Distance: 1.5
  6. Click the From beginning button or press the F4 key on your keyboard to begin applying the recipe to the image

You will see two object set outputs: Cross Sections and Surfaces. The Cross Sections output allows you to view the cross section outline of the detected objects in 2D view; the Surfaces output allows you to view the surface reconstructions of the detected objects in 3D view.

Results
3DObjAnalysisDemo_z62_t000_XSections.png
2D Cross Sections (at z=62)

3DObjAnalysisDemo_z62_t000_3Drecon.png
3D Surfaces


Image Credits


Philipp Keller, Howard Hughes Medical Institute, Janelia Farms Research Campus; Cell Tracking Challenge,
http://www.celltrackingchallenge.net/datasets.html