Embedding MotiQ plugins in your own ImageJ Macro

Can I embed MotiQ plugins into an ImageJ macro?

Yes, you can, and thereby make use of MotiQ plugins in your own analysis pipeline and combine them easily with other ImageJ functions or plugins.

You can use ImageJ's / FIJI's macro recorder (started in ImageJ or FIJI via the menu entry Plugins > Macros > Record) to record the macro command to run MotiQ Thresholder, MotiQ 2D Analyzer, or MotiQ 3D Analyzer under the settings of your choice:

Or you can write a command yourself using the key words shown in the example macro commands below.

• To deselect the boolean commands such as local-threshold or include-date simply remove them from the command string.
• Insert the values of your choice for string, selection, or number parameters. E.g., you can customize the minimum-particle-area key word from minimum-particle-area=50 to minimum-particle-area=100 to increase it to 100. However, do not omit the square brackets where they are used!
• If you miss out specifying a string, selection, or number parameter, the default parameter value will be applied.

run("MotiQ Thresholder (v0.2.1)", "use-alternate automatically-find begin-of-suffix=[_CUT] additional-suffix=[.tif] restrict scale=0.5 convert threshold=MinError stack-handling=[apply threshold determined in a maximum-intensity-projection] threshold-every-time-step threshold-only-distinct-times start-time=1 end-time=10 local-threshold local-threshold-radius=5 fill-holes keep-intensities automatically-save include-date");

run("MotiQ 2D Analyzer (v0.2.1)", "re-calibrate length=0.5 calibration-unit=micron time-interval=0.10 time-unit=min minimum-particle-area=50 remove-all-but-largest time-steps-grouped=12 calculate=[every particle seperately (track particles by overlap)] skeleton=[derive skeleton data from a BINARIZED copy of the input image] gauss=1.0 number-format=[US (0.00...)] include-date");

run("MotiQ 3D Analyzer (v0.3.1)", "re-calibrate length=0.4170 depth=1.0000 calibration-unit=um time-interval=0.50 time-unit=min minimum-particle-volume=50 time-steps-grouped=10 calculate=[all detected particles merged into one object] skeleton=[derive skeleton from a copy of the input image] gauss-xy=1.0 gauss-z=0.0 number-format=[US (0.00...)] include-date");