Missing blob diameter in trackmate macro

Dear all,

I am getting started with imageJ macros and I get to process single-molecule movies but I have realised when checking the results that trackmate did not consider the blob radius for the analysis, although is present in the code.

Here is the code

//TrackMate parameters
Dialog.create("Parameteres");
  Dialog.addMessage("Parameters for the POI in nm");
  Dialog.addNumber("Blob_radius", 200);
  Dialog.addNumber("Threshold", 100);
  Dialog.addNumber("Spot_distance", 321);
  Dialog.addNumber("Gap_distance", 200);
  Dialog.addNumber("Gap_frame", 4);
  Dialog.addNumber("track_filter", 5);  
  Dialog.show();
  Blob_radius =  Dialog.getNumber();
  Threshold =  Dialog.getNumber();
  Spot_distance =  Dialog.getNumber();
  Gap_distance =  Dialog.getNumber();
  Gap_frame =  Dialog.getNumber();
  track_filter = Dialog.getNumber();

//Open first movie
roiManager("reset")
waitForUser("File loading", "Open the SM movie, then OK")
M1 = getInfo("image.filename")
close()

					//  ------> Analysis <----------
//Movie 1
open(SM_path+"/"+M1)
	run('TrackMate', "use_gui=false"
	+ "radius="+Blob_radius+" "
    + "threshold="+Threshold+" "
    + "subpixel=true "
    + "median=true "
    + "channel=1 "
    + "max_distance="+Spot_distance+" "
    + "max_gap_distance="+Gap_distance+" "
    + "max_frame_gap="+Gap_frame+" " 
    + "filter_tracks_nspots_above="+track_filter+" " 
    + "save_to=["+TM_path+"/"+M1+"_all.xml] ")

All the rest of the parameters have worked fine.

Thank you in advance for your help

@Hector_Romero

Perhaps try adding a ‘space’ after "use_gui=false"? So make it "use_gui=false ". Does that do it?

2 Likes

Hi @etadobson,

Thank you for your answer, it was really this!

I did not expect to be something like this, as all the other features were shown correctly.

1 Like