Volker Bäcker, uses the Watershed plugin from Christopher Mei.
Example
The application counts the number of objects in an image, measures each object and writes the measurements per object and the mean values per image into a spreadsheet-file. When the application is started the list-editor is opened. Press the add button and select the files you want to measure. Press close on the list editor to start. You will be asked where to save the result spreadsheet file.
To change options either press the O-button of the application or open the application (right click on the top of the application tile and select open from the context menu) and press the O-button of one operation of the application.
Important options are smoothing diameter, and the min. size and max. size.
The smoothing diameter is 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.
The min. and max. size can be used to eliminate wrong objects that are either too small or too big. The area of the objects you want to measure must be between the min. and the max. value.
For each image a control-image showing the nuclei that have been taken into account is written into the sub-folder named count-nuclei-control of the folder containing the input images.
The number of objects per image, the mean area of all objects per image and the area and coordinates of all objects are written into a spreadsheet-file.