Foci Per Nucleus Tool
The tool detects, counts and measures the foci per nucleus. It reports the number of small, medium sized and big fosci per nucleus. It also measures the area and mean intensity of the nuclei.
To install the tool save the file foci_per_nucleus_tool.ijm under macros/toolsets in your FIJI installation.
Select the foci_per_nucleus_tool toolset from the >> button of the ImageJ launcher.
- The first button on the toolset opens this help page.
- The
m-button runs the foci-analysis on the current image. - The
b-button runs the foci-analysis on all the images in a given folder.
Open the options-dialog by right-clicking on the m-button.
- threshold one and threshold two
- The numbers of foci with an area below threshold one, between threshold one and threshold two and above threshold two will be reported
- scale factor
- The nuclei are detected on a down-scaled image, this is the factor by which the image is reduced in size for the nuclei segmentation. If over--segmentation occurs, try a higher factor
- min. area
- Objects detected during the nuclei segmentation, which have a smaller area than min. area will be eliminated from the analysis.
- nuclei thresholding method
- The auto-treshold method used for the segmentation of the nuclei.
- sigma of Gaussian blur filter
- During the segmentation of the foci a blurred version of the image is subtracted from the original image to eliminate the nuclei and the background. This parameter is the sigma of the Gaussian blur filter used.
- min. prominence of maxima
- A seeded watershed is used to separate touching foci. Local maxima in the image are used as seeds. The parameter gives the min. prominence of a maximum from the background to be used as a seed
- foci thresholding method
- The auto-threshold method used for the segmentation of the foci.
Open the options-dialog by right-clicking on the b-button.
- file extension
- The file-extension of the image-files that will be processed in the batch-processing.
Volker Bäcker