Recipe Description


The Colony Analysis recipes 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 routines for each. The recipe measures the morphology of the detected colony regions.



Parameters and Presets


Parameters

Parameters and their descriptions for the recipe are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Colony Detection
Colony Detection Sensitivity
0
255
Adjusts the sensitivity of the detection; a lower value will detect bigger and more objects; the MEF substrate and Matrigel substrate options lets you select different detection routines depending on your plating substrate
Colony Refinement
Minimum Colony Area
0
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
Colony Refinement
Fill Holes Size
0
10,000,000
Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
Colony Refinement
Smoothing Factor
0
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 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

Colony Refinement

Parameter Name
Small
Medium
Large
Minimum Colony Area
25,000
50,000
200,000
Fill Holes Area
5,000
10,000
50,000
Smoothing Kernel
15
25
35

Measurements


The Colony Analysis recipes 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
    • Area
    • Circularity
    • Normalized Area
    • Normalized Confidence
  • Intensity (measured on the input channel)
    • Mean
  • Summary
    • 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 (ColonyDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.
  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 caret.png 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 in tact
    • Minimum Colony Area: 25,000
  6. Click the From beginning 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
ColonyDemo_output.png
Colony Analysis results