Aivia Software
Colony Analysis
The Colony Analysis recipe in Aivia detects colonies in phase contrast microscopy images and measures the morphology of the detected colony regions.
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 substrate.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Colony Analysis and their descriptions 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 let you select different detection routines depending on your plating substrate |
Colony Refinement | Minimum Colony Area | 0 | 1,000,000,000 px2 or µm2 | Specifies the minimum size for objects to be included in the analysis results based on the areas of the detected objects |
Fill Holes Area | 0 | 10,000,000 px2 or µm2 | Adjusts the maximum size threshold for filling in gaps inside detected objects; a lower value will preserve more holes in the detection | |
Smoothing Factor | 0 | 100 | Adjusts the amount of smoothing applied to the outlines of the detected objects; a lower value will preserve more of the objects' 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 Area | 5,000 px2 or µm2 | 10,000 px2 or µm2 | 50,000 px2 or µm2 |
Smoothing Factor | 15 | 25 | 35 |
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 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
F4key on your keyboard to begin applying the recipe to the image.
The detected object outlines will be overlaid on the image.
Measurements
The Colony Analysis recipe generates morphological and count measurements for detected colony regions. You can add additional measurements to the analysis results with the Measurement Tool and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are as follows:
Morphology | Count |
|---|---|
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