pixFRET - 运行插件的时间推移图像/ /循环？

我没有找到一种方法，包括直接从pixFRET插件参数和命令。然而，在这里我展示了一个与IJ_Robot一起工作的工作来添加这些命令。我还根据时间序列的第一张图像，添加了一些东西来执行相机通道的对齐。

// Macro for creating time resolved pixFRET images with a alignment of both cameras used 
// a separate setting file is required for pixFRET -> put this into the same folder as the pixFRET plugin 
// the background region has to be set manually in this macro 
// IJ_robot uses cursor movements - DO NOT move the cursor while excuting the macro + adjust IJ_robot coordinates when changing the resolution/system. 
dir = getDirectory("Select Directory"); 
list = getFileList(dir); 
//single alignment 
run("Image Sequence...", "open=[dir] number=2 starting=1 increment=1 scale=100 file=[] or=[] sort"); 
rename(File.getName(dir)); 
WindowTitle=getTitle() 
rename(WindowTitle+toString(" Main")) 
MainWindow=getTitle() 
NSlices=getSliceNumber() 
xValue=getWidth()/2 
yValue=getHeight()/2 
//setTool("rectangle"); 
makeRectangle(0, 0, xValue, yValue); 
run("Align slices in stack...", "method=5 windowsizex="+toString(xValue*2-20)+" windowsizey="+toString(yValue*2-20)+" x0=10 y0=10 swindow=0 ref.slice=1 show=true"); 
selectWindow("Results"); 
XShift=getResult("dX", 0); 
YShift=getResult("dY", 0); 
File.makeDirectory(toString(File.getParent(dir))+toString("\\")+"test"+" FRET"); 
for(i=0;i<list.length;i+=4){ 
open(dir+list[i+1]); 
run("Translate...", "x=XShift y=YShift interpolation=None stack"); 
open(dir+list[i]); 
open(dir+list[i+3]); 
run("Translate...", "x=XShift y=YShift interpolation=None stack"); 
wait(1000); 
run("Images to Stack", "name=Stack title=[] use"); 
selectWindow("Stack"); 
makeRectangle(15, 147, 82, 75); //background region 
run("PixFRET..."); 
run("IJ Robot", "order=Left_Click x_point=886 y_point=321 delay=500 keypress=[]"); 
run("IJ Robot", "order=Left_Click x_point=874 y_point=557 delay=500 keypress=[]"); 
selectWindow("NFRET (x100) of Stack"); 
save(toString(File.getParent(dir))+toString("\\")+"test"+" FRET"+toString(i) +".tif"); 
selectWindow("Stack"); 
close(); 
selectWindow("FRET of Stack"); 
close(); 
selectWindow("NFRET (x100) of Stack"); 
close(); 
run("IJ Robot", "order=Left_Click x_point=941 y_point=57 delay=300 keypress=[]"); 
} 

感谢您的帮助一月如果你能想到的方法来调用这些pixFRET直接命令，而不是使用Ij_robot，请让我知道。

采取从Fiji (is just ImageJ)this tutorial为出发点，并使用宏录制（插件>宏>记录...），以获得neccessary命令。然后

宏代码可能是这个样子：

function pixfret(path, commonfilename) { 
    open(path + commonfilename + "c2"); 
    open(path + commonfilename + "c1"); 
    open(path + commonfilename + "c4"); 
    run("Images to Stack", "name=Stack title=[] use"); 
    run("PixFRET"); // please adjust this to your needs 
} 
setBatchMode(true); 
n_timepoints = 999; 
dir = "/path/to/your/images/"; 
for (i = 0; i < n_timepoints; i++) 
    pixfret(dir, "filename_t" + IJ.pad(i, 4)); 
setBatchMode(false); 

希望有所帮助。