Counting toolset

Button1: Open the “Cell Counter” (Kurt De Vos) for manual counting.

Button2: Run the “Count Nuclei Watershed” application.
Adds the objects it found on the current image to the roi-manager.

Button3: Run the “Count Nuclei Watershed Batch” application.
Lets the user select the input images, counts the nuclei per image in batch mode and writes results into a spreadsheet file.

Button4: Run the “Count Nuclei Watershed Interactive” application.
Works like the previous application, but lets the user control and eventually correct the nuclei found for each image.

A right click on one of the buttons 2-4 opens the options dialog for the application.

Author:

Volker Baecker

Example

Description

The applications 2-4 will find and count objects in images, using a watershed algorithm to separate touching objects.

Options


Radius of smoothing filter: The radius of the kernel of a smoothing filter that is applied before the watershed. It needs to be big enough to make disappear internal structures of the objects you want to count, since otherwise objects will be split too much. It should not be bigger than necessary since otherwise the contours of the objects become imprecise and touching objects may not be split.
Min. size of nucleus: Objects smaller than the min. size will not be taken into account.
Max size of nucleus: Objects bigger than the max. size will not be taken into account.