How to optimize the cell segmentation process

To get a fresh start, reset all the attributes using the reset button

Test the settings and look at the particles

Attribute values are displayed in the image, adjacent to each detected particle—Zoom In

Fine tune the attributes to reject any particle that is not within your criteria for an individual cell

Rejected particles (red) can be segmented subsequently

Usually, it is recommended that you define at least a range of areas, widths and lengths

In some cases you might also need to define a range of angularities to exclude some touching cells

In order to automatically segment the rejected particles, select the segmentation option and test the settings again

During the segmentation process, a set of methods/filters are used in parallel to segment the rejected particles

For each rejected particle, the method maximizing the number of particles that are within your criteria is chosen

If none of these methods produce particles within your criteria, the rejected particle is not segmented

There are two reasons why this happens:

Either the different methods have not been able to segment the particles inside the rejected particle

Or because the segmented particles are not within your criteria

To help you sort through those two possibilities, you can access the outcome of each method using the segmentation panel

Select the rejected cell that has not been segmented using a ROI and click on the test button in the segmentation panel

This will open an image window with the original particle contour and the different outcomes of each method.

Look at the different particles, fine tune the attributes and test the settings again

If you obtain the particles segmented within your criteria you can move on to the options and generate the result

If you still have unsegmented particles you can move on to the options and use the manual editor, which we cover in the next tutorial

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