What are the differences in the Algorithms in the PIXL software?

Introduction

The following sections explain the different algorithms used in the PIXL Software.

Background Subtraction

A simple background removal for plates with high colony/agar Contrast. This will not separate touching colonies. A faster algorithm for easily distinguishable colonies, it's speed allows large numbers of colonies to be detected, but you can also see artefacts as it is not highly selective. Tip: Artefacts have low 'intensity' scores, by adding a small intensity filter from the low end of the scale, you will eliminate this noise. 

Adaptive Detection

Designed to work for images with low colony/agar contrast. Touching colonies will be separated. This is better suited to more troublesome colony selection, effectively it forms a histogram of the plate, and looks for pixel distributions that stand out from the relative background. Hence 'adaptive'.

Colony Separation

Designed to separate touching colonies. This works best with high colony/agar contrast. When you have clearly defined circular colonies, and it is important to be able to separate those that are touching, this algorithm should be the one to choose. It attempts to fit circles on the foreground of the image, thus colonies with odd morphologies may give strange results. This feature also makes the computation relatively slow, if you are detecting thousands of colonies, this can make the PIXL appear as if it has 'hung' on the colony detection screen - it hasn't! It's simply working away.

Specific Detection

A series of detection filters, each design to deal with a specific, difficult-to-detect organism. This was devised in order to deal with edge cases, such as colonies that are highly 'shiny' reflecting the LED banks of the PIXL, or both low and high contrast colonies on the same plate. It effectively uses a mixture of the above algorithms and compares the results, also changing the image in several ways. Of all the choices, this one may produce the oddest results! They were normally designed with 'specific' cases in mind, hence the name. If a custom development is requested, and it's a tough nut to crack - it normally finds itself as a sub-selection of this mode.

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