The tool detects spots and measures the nearest neighbour distances between the spots in the image.

You can download an example image here: spots.tif

The source code in git-hub can be found here.

You must have FeatureJ installed.

To install the tool save the two files find_nearest_neighbors.py and spot_distances_tool.ijm into the folder macros/toolsets of your FIJI installation.

Select the "spot_distances_tool" toolset from the >> button of the ImageJ launcher.

• the first button (the one with the image) opens this help page
• the a-button runs the analysis on the active image
• the b-button runs a batch-analysis on a folder containing the input images

Spots are detected, using a LoG-filter (FeatureJ Laplacian) with a sigma calculated from the mean radius r of the spots provided by the user: σ = r / sqrt(2). ImageJ's Find Maxima command is used to detect the spots as the minima in the image resulting from the LoG-filter. A python (jython) script is used to calculate the nearest neighbour distances.

Right click on the a-button to open the options-dialog.

spots channel

the channel containing the spots

spots z-slice

the z-slice containing the spots

av. spot radius

the average radius of the spots will be used to calculate the sigma for the LoG-filter

proeminence

the noise tolerance for the Find Maxima-command.

correct manually

if selected the execution is paused after the spot detection step and the user can manually correct the spots

Right click on the b-button to open the batch-options-dialog.

image-file-extension

the file extension of the image-files (tif, czi, ...)