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.
Measurements
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
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
to 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 objects outline and tracks 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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