Colony Analysis

The Colony Analysis recipe in Aivia detects colonies in phase contrast microscopy images. The recipe can be used for detecting colonies that are plated on substrate layers containing mouse embryonic fibroblasts (MEF) or Matrigel with optimized detection routines for each. The recipe measures the morphology of the detected colony regions.

Parameters and Presets


Recipe parameters for Colony Analysis and their descriptions are summarized in the table below.

Preset GroupParameter NameMin ValueMax ValueDescription
Colony Detection

Colony Detection Sensitivity


Adjusts the sensitivity of the detection; a lower value will detect bigger and more objects; the MEF substrate and Matrigel substrate options let you select different detection routines depending on your plating substrate

Colony Refinement

Minimum Colony Area01,000,000,000Specifies the minimum size for objects to be included in the analysis results based on the area of the detected objects
Fill Holes Size01,000,000Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
Smoothing Factor0100Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features


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

Colony Detection

Parameter NameLowMediumHigh
Colony Detection Sensitivity20105

Colony Refinement

Parameter NameSmallMediumLarge
Minimum Colony Area25,00050,000200,000
Fill Holes Size5,00010,00050,000
Smoothing Factor152535


The Colony Analysis recipe generates morphological and intensity measurements for detected colony regions. Normalized morphological measurements are included to account for the size difference between colonies. 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:

  • Area
  • Circularity
  • Normalized Area
  • Normalized Confidence
  • Mean
  • Colony Area Mean
  • Colony Area Maximum
  • Colony Area Minimum
  • Colony Circularity Mean
  • Colony Circularity Maximum
  • Colony Circularity Minimum


Before beginning the tutorial, please download the Colony 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, ColonyDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the Colony Analysis recipe
  3. Select the Low preset for the Colony Detection group and the Medium preset for the Colony Refinement group
  4. Click on the caret  to the left of the Colony Refinement preset group to show the preset parameters
  5. Modify the parameter values as follows, leaving the other parameters intact:
    • Minimum Colony Area: 25,000
  6. Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image

The detected objects outline and tracks will be overlaid on the image.


Colony Analysis results