Count the number of axonal projections that cross a given line. The tool detects and counts the maxima along a line-selection, for example a segmented line.

To install the tool save the file count_axonal_projections.ijm into the folder macros/toolsets of your FIJI installation.

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

• the first button opens this help page
• the c-button runs the tool on the active image, which must have a line-selection

Draw a line-selection (for example a segmented line) on the image and press the c-button. You can change the width of the line selection (double-click on the line-selection tool-button), before running the tool. If the line-width is smaller than 2, the tool will use a line width of 2.

auto detect threshold

if selected the mean value in the selection is used as a global threshold for the maxima

threshold

if auto detect threshold is not selected, this threshold value is used

auto detect tolerance

if selected half of the standard deviation is used as tolerance value for the maximum detection

tolerance

if auto detect tolerance is not selected, this tolerance value is used