run("Action Bar","/plugins/ActionBar/_ActionbarSA.txt"); exit(); label=Register images to first icon=noicon arg= showMessage("This one isn't done yet"); //doCommand("Register"); path = getDir("plugins"); string = exec(path+"\\ConsoleApp1"); showMessage(string); label=Toggle Machine-marked objects icon=noicon arg= ojShowImage(1); tog = call("ij.Prefs.get", "pre.qual_tog", "this is wrong"); lis = call("ij.Prefs.get", "pre.val0", "this is wrong"); for(i = ojFirstObject(1); i <= ojLastObject(1); i ++){ ojSelectObject(i); obId = ojIndexToId(i); if(tog==false){ ojQualify(i, true); }else if(tog==true && lis.contains(toString(obId))){ ojQualify(i, false); } } if(tog==false){ call("ij.Prefs.set", "pre.qual_tog", true); //these are for the next time the macro is called }else if(tog==true){ call("ij.Prefs.set", "pre.qual_tog", false); } label=select Marker and ROI icon=noicon arg= n = obj_num = getNumber("enter object number: ", 1); run("3D Manager"); nb_obj = 0; Ext.Manager3D_Count(nb_obj); if (nb_obj==0){ showMessage("There are no regions in the 3d ROI manager"); }else{ run("3D Manager"); Ext.Manager3D_DeselectAll() Ext.Manager3D_MultiSelect(); for(i = 0; i < nb_obj; i ++){ name = ""; Ext.Manager3D_GetName(i, name); name = split(name, "-"); if(name[0].contains(n)){ Ext.Manager3D_Select(i); } } Ext.Manager3D_MonoSelect(); } ojSelectObject(n); ojShowObject(n); label=Update ObjJ markers icon=noicon arg= showMessage("Select location of object marker lists"); path = getDir("Location of object marker lists"); image_num = getNumber("image number:", 1); ojShowImage(image_num); numRows = getValue("results.count"); IJ.deleteRows(0,numRows); if(is("composite")){ }else{ row = 0; start = ojFirstObject(image_num); end = ojLastObject(image_num); for (i = start; i <= end; i++, row++) { ojSelectObject(i); name = ojGetItemName(); x = ojXPos(1); y = ojYPos(1); z = ojZPos(1); setResult("X", row, x); setResult("Y", row, y); setResult("Z", row, z); } saveAs("Results", path+"chan1_model.csv"); } showMessage("new lists saved in project folder"); run("Close"); label=Run Simple Neurite Tracer icon=noicon arg= cellfill = getNumber("enter channel number of cell fill", 1); ojShowImage(1); run("Duplicate...", "duplicate channels="+cellfill); run("Simple Neurite Tracer"); label=Delete objects in image icon=noicon arg= image_num = getNumber("image number: ", 1); ojShowImage(image_num); while(ojLastObject(image_num)-ojFirstObject(image_num)>=0){ n = ojFirstObject(image_num); ojDeleteObject(n); } label=Identify objects in first image icon=noicon arg= ojSetComposite(false); if(ojNObjects()==0){ doCommand("MarkerGuesser"); //run("MarkerGuesser");? }else if(ojNObjects()>0){ redo = getBoolean("There are already objects marked. Redo and delete all objects in all images?"); if(redo == true){ ojDeleteAllObjects(); doCommand("MarkerGuesser"); } } //after, just qualify all of the objects? label=Measure Intensity icon=noicon arg= ojShowImage(1); marker_channel = getNumber("channel to use to ROI: ", 1); obj_size = getNumber("radius of objs: ", 15); num_objs = ojNObjects(); height = ojGetImageValue(1, "height") ; width = ojGetImageValue(1, "width") ; stacksize = ojGetImageValue(1, "stacksize") ; name = ojGetImageName(1); name = replace(name, ".tif", ""); ojShowImage(1); run("Duplicate...", "duplicate channels="+marker_channel+""); rename("duplicate1"); run("8-bit"); for(n = 1; n <= num_objs; n ++){ ojSelectObject(n); ojName = ojGetItemName(); x = ojXPos(1); y = ojYPos(1); z = ojZPos(1); if(z%3==marker_channel || (z%3)+3==marker_channel){ stack_z = ((z/3)); run("3D Draw Shape", "size="+width+","+height+","+(stacksize/3)+" center="+x+","+y+","+stack_z+" radius="+obj_size+","+obj_size+","+obj_size+" vector1=1.0,0.0,0.0 vector2=0.0,1.0,0.0 res_xy=1.000 res_z=1.000 unit=pixels value=255"); run("3D Intensity Measure", "objects=Shape3D signal=duplicate1"); selectWindow("Shape3D"); run("3D Manager"); Ext.Manager3D_AddImage(); selectWindow("duplicate1"); close("\\Others"); } } selectWindow("Results");