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The 3D Object Analysis - Meshes and 3D Object Analysis - Spots recipes in Aivia detect objects (such as cells and nuclei) in 3D volumetric images.

The 3D Object Analysis - Meshes recipe creates surface reconstructions of all detected objects.

The 3D Object Analysis - Spots recipe creates spot representations of objects. Spots are spherical objects with fixed size that lower the rendering cost for visualizing object counts and positions.


On this page:

Table of Contents
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Automatic Parameter Selection

ATL (Aivia That Learns) and the Auto Icon

3D Object Analysis - Meshes features AI-powered automatic parameter selection (sometimes referred to as Aivia That Learns, or ATL). This is an internal model, trained by human experts, that given the selected input image channel, predicts the parameters and populates the Recipe Console with predicted parameters.

There are two ways that ATL is activated for 3D Object Analysis:

  • By clicking the 3D Object Analysis purple tile in the search bar (see below). ATL is activated and predicts all the parameters of the recipe automatically. This mode had the advantage that you can try to preview the result in the selected ROI, with just two clicks (first the purple tile, then on Preview, the Magnifier lens besides the description of the parameters).

  • Click on the Auto icon (see figure to the right) in the recipe header to initiate the parameter prediction.

Quick advices for using automatic selection

  1. Image Smoothing Filter Size and Mesh Smoothing Factor are parameters that affect the smoothness of the final mesh. ATL might not predict these parameters, so you can experiment with them after running the recipe with ATL-generated parameters. Try small increments of the values and check in the preview to achieve nicer visualization of the current segmentation. We recommend using Image Smoothing Filter Size if you observe the image is noisy, and Mesh Smoothing Factor to increase the smoothness the final mesh (less irregularities and peaks).

  2. ATL gives you a suggestion for parameters but occasionally may yield less than perfect results due to noise in data, variations on brightness and contrast etc. You might use ATL-generated values as starting point, then check in the Recipe console about the different parameters that can be adjusted to fine-tune the results. There are three possible cases when the prediction might yield less than ideal results:

  • Only a few objects are displayed: An image might be very heterogeneous (has objects of multiple sizes, both very big and very small or has low SNR). In this case, some objects might be shown while others are missing. A good starting place is first to modify the Min Edge Intensity (reduce it to around 30%), then the Object Radius (min radius value can be smaller and max radius value can be bigger), and finally the Min Edge to Center Distance (only if applies because Partition was selected, as a rule of thumb, it must be the average size of the object of interest). Other parameters might need further adjustment to refine the resultant segmentation.

  • Too many objects are displayed: Similar to the option above, modify first the Min Edge Intensity (increase it to around 10% each time until satisfied), then the Min Edge to Center Distance (if applies), and if you want to crop out small objects, the Object Radius (min value). Other parameters might need further adjustment to refine the resultant segmentation.

  • No results are shown in preview: Start modifying the Min Edge Intensity by putting half the value shown in the prediction. If it does not work, keep reducing the value. If you arrive to 0 in intensity, check the Min and Max value of the Object radius.

3D Object Analysis Active Tile

Another way to initiate parameter estimation for 3D Object Analysis - Meshes is through the 3D Object Analysis Active Tile, which is accessed from the search bar at the top of the Aivia window.

The 3D Object Analysis Active Tile also adjusts the Aivia layout to one that is recommended for an object analysis workflow and creates and/or selects a region of interest (ROI) that may be useful for previewing and evaluating the parameters.

Parameters and Presets


Recipe parameters for 3D Object Analysis - Meshes/Spots and their descriptions are summarized in the table below.

Preset Group

Parameter Name

Min Value

Max Value



Image Smoothing Filter Size

(without Skip Smooth Image only)



Specifies the diameter of the filter that is used to smooth the input channel before further processing

The available smoothing types are the following:

  • Morphological Smoothing applies a morphological filter consisted of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size.

  • Average Filter Smoothing applies an average filter that outputs the average intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size.

  • Gaussian Filter Smoothing applies a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size.

  • Median Filter Smoothing applies a median filter that outputs the median intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size.

Average Object Radius

(Remove Background only)


1,000 px or µm

Specifies the radius of a typical object in the image for object enhancement and background removal; a lower value will preserve smaller objects

Min Edge Intensity


255 (8-bit)

65,535 (16-bit)

Specifies the minimum object intensity that is typically found 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

Fill Holes Size


1,000,000 px2 or µm2

Specifies the maximum size of gaps in detected objects that are filled; a lower value leads to the preservation of more holes in the detected objects


Object Radius


50,000 px or µm

Specifies the range of objects to be included in the analysis results based on the radii of the detected objects

Mesh Smoothing Factor

(3D Object Analysis - Meshes only)



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

Min Edge to Center Distance

(Apply Partition only)


1,000 px or µm

Specifies the minimum distance from the center of an object to the edge that is touching its closest neighboring object; a lower value will apply object partitioning more aggressively, resulting in smaller, more uniform objects


There are two preset groups in the recipe: Detection and Partition. Each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are given in the sections to follow.


Parameter Name




Image Smoothing Filter Size




Average Object Radius

5 px or µm

20 px or µm

100 px or µm

Min Edge Intensity

51 (8-bit)

31 (8-bit)

10 (8-bit)

13,107 (16-bit)

7,864 (16-bit)

2,621 (16-bit)

Fill Holes Size





Parameter Name




Object Radius

2 - 5 px or µm

20 - 50 px or µm

100 - 300 px or µm

Mesh Smoothing Factor




Min Edge-to-Center Distance

2 px or µm

20 px or µm

100 px or µm

Tutorial (written steps)

Before beginning the tutorial, please download the 3D Object Analysis Demo image. For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console.

  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 - Meshes recipe.

  3. Click on the Show Advanced Interface icon (see right) to expand the Recipe Console.

  4. Click on the second Switch Recipe Operations icon (see right) to show a list of available recipe operations; select the Remove Background option from the dropdown menu.

  5. Select the following settings for the recipe:

    • Image Smoothing Filter Size: 9

    • Average Object Radius: 5

    • Min Edge Intensity: 5

    • Fill Holes Size: 2

    • Object Radius: 2 - 6

    • Mesh Smoothing Factor: 2

    • Min Edge to Center Distance: 1.5

  6. Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image.

You will see one object group with two object sets as outputs:

  • The Meshes output allows you to view the surface reconstructions of the detected objects in 3D View.

  • The Cross Sections output allows you to view the cross sections of the detected objects in Main View (2D).


Tutorial (video)



The 3D Object Analysis - Meshes 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 and explore measurement definitions on the Measurement Definitions page. The measurements generated by the meshes version of the recipe are given in the table below.




  • Surface Area

  • Volume

  • Mean Intensity

  • Max Intensity

  • Min Intensity

  • Total Intensity

  • Std. Dev. Intensity

  • Object Count

The 3D Object Analysis - Spots recipe also generates a count of the total number of objects in the group but only generates a few other measurements, which are related to position, since spots do not necessarily capture the morphology or intensity of objects. The measurements generated by the spots version of the recipe are given in the table below.



  • Centroid X

  • Centroid Y

  • Centroid Z

  • Object Count

Image Credits

Philipp Keller, Howard Hughes Medical Institute, Janelia Farms Research Campus, Ashburn VA; Cell Tracking Challenge,

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