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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.

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Table of Contents

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Parameters and Presets

Parameters

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

Preset Group	Parameter Name	Max Value	Description
Colony Detection	Colony Detection Sensitivity	255	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 Area	1,000,000,000 (px² or µm²)	Specifies the minimum size for objects to be included in the analysis results based on the area of the detected objects
	Fill Holes Area	1,000,000 (px² or µm²)	Adjusts the maximum size threshold for filling in gaps inside

a

detected

object

objects; a lower value will preserve more holes in the detection
Smoothing Factor	0	100	Adjusts the amount of smoothing applied to the

outline

outlines of the detected objects; a lower value will preserve more of the

object

objects'

s

morphological features

Presets

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 in the sections to follow.

Colony Detection

Parameter Name	Low	Medium	High
Colony Detection Sensitivity	20	10	5

Colony Refinement

Parameter Name	Small	Medium	Large
Minimum Colony Area	25,000 (px² or µm²)	50,000 (px² or µm²)	200,000 (px² or µm²)
Fill Holes

Size

Area	5,000 (px² or µm²)	10,000 (px² or µm²)	50,000 (px² or µm²)
Smoothing Factor	15	25	35

Measurements

The Colony Analysis recipe generates morphological and intensity count measurements for detected colony regions. You can add additional measurements to the analysis results by using with the Measurement Tool in Aivia. The measurements generated by the recipe are as follows:

Morphology	Count
Area	Component Count

Tutorial

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.

Unzip the demo file and load the demo image, ColonyDemo.tif, into Aivia
In the Recipe Console, click on the Recipe selection dropdown menu and select the Colony Analysis recipe
Select the Low preset for the Colony Detection group and the Medium preset for the Colony Refinement group
Click on the

caret

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caret to the left of the Colony Refinement preset group to show the preset parameters
Modify the parameter values as follows, leaving the other parameters intact:
- Minimum Colony Area: 25,000
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 object outlines will be overlaid on the image.

Colony Analysis results

Results

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Versions Compared

Old Version 9

New Version 10

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