Aivia Software

Mesh display

Meshes, or surfaces, are representation of objects in 3D View. They can be generated several ways, such as the following:

This page covers display options that are specific to meshes. General information on displaying object sets can be found on the Object Settings page.


Object groups that are of the mesh type can appear in the Object Set Settings panel as shown below. 

The object group displayed above was created by a recipe and includes an object set called "Cross Sections" that appears only in Main View (2D).

Some recipes output spots as simplified representations of 3D objects; these spots have a Set Spot Radius option  to the left of the Export Objects to a Mask icon .

On this page:

Rendering modes

You can specify the rendering mode for object sets and groups in 3D View using the icon in the View column. There are three (3) rendering modes available:

Rendering ModeIconDescription
Solid Surface

Renders meshes as solid, closed surfaces

Renders meshes as sets of connected line segments

Renders meshes as point clouds

Once a new rendering mode is selected, the displayed object sets are refreshed automatically to reflect the new selection.

Depending on your hardware, the size of the image, and the rendering mode chosen, it may take Aivia up to several minutes to fully render the display with the specified settings.

A comparison between the three (3) rendering-mode displays is shown below (click on an image to enlarge it).

Solid SurfaceWireframePoints

Rendering-mode options


The percent transparency of an object set is indicated in the Alpha column of the Object Set Settings table. Click on the percentage in the Alpha column to show a slider that can be used to adjust the transparency of the object set. 

Transparent (lime green and blue) and opaque (pink and mint green) meshes

Coloring options

The coloring mode can be specified by clicking on the icon in the Color column of the Object Set Settings table. There are six (6) available coloring modes for meshes; all modes are summarized in the table below in addition to Color By Cell mode, which is only available for whole-cell mesh/spot groups that are created by the 3D Cell Analysis recipe.

Coloring ModeIconDescriptionExample (click to enlarge)
Solid Color

Applies the same color to all objects

Color By Label

Applies different colors to each object according to the object labels

Color By Object Type

Applies the same color to all objects that are of the same object type

Color By Name

Applies different colors to each object according to the object names

Color By Measurement

Applies different colors to each object based on values for a user-specified measurement

Color By Class

Applies different colors to each object based on object classifications

Color By Cell

(only for whole-cell object groups)

Applies different colors to each cell, keeping all components (cell membrane, nuclear membrane, and vesicles) of a given cell the same color

Image credits

Jocelyn Fadiga and Todd Nystul, University of California San Francisco - Parnassus Campus, San Francisco CA