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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 detecting detection routines for each. The recipe measures the morphology of the detected colony regions.

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Table of Contents

maxLevel	3
exclude	[4]

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 lets let you select different detection routines depending on your plating substrate
Colony Refinement	Minimum Colony Area	1,000,000,000	Specifies the minimum size for objects to be included in the analysis results based on the area of the detected objects
	Fill Holes Size	1,000,000	Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
	Smoothing Factor	100	Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features

Presets

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

Colony Detection

Parameter Name	Low	Medium	High
Colony Detection Sensitivity	20	10	5

Measurements

The Colony Analysis recipes 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:

Morphological	Intensity	Summary
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

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 Image Modified to the left of the Colony Refinement preset group to show the preset parameters
Modify the parameter values as follows: , leaving the other parameters in tactintact:
- Minimum Colony Area: 25,000
Click the From beginningStart 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.

Results

Image Modified

Colony Analysis results

Versions Compared

Old Version 6

New Version 7

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