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_DKR_Hotkey_Annotate_Image.ijm
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_DKR_Hotkey_Annotate_Image.ijm
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// 20140905 ciclistadan
// annotate an image, record counts of each marker in results table, ability to save roi/crop of each
//
// This macro makes use of lettered hotkeys, and therefore assumes that "Require control key for shortcuts"
// in Edit▷Options▷Misc…↓ is checked.
//
// a = infected + granules (AVG)
// s = uninfected + granules (SG)
// d = uninfected cell without granules
// f = infected cells (with factory)
// 1/2/3 toggle channels
// r = refresh annotations on display
// p = print results to Results window
// o = output results and roi
function mark();
macro "initialize" {
// if(nImages>1) exit ("close all but one image before proceeding");
// getDimensions(imageWidth, imageHeight, channels, slices, frames);
// if(slices>1) exit ("this image has "+slices+"slices'n"+"this macro requires a single flat image (no z-stacks)");
name=getTitle();
basename = substring(name,0,lengthOf(name)-4);
roiManager("Reset");
roiManager("Show All with labels");
run("Labels...", "color=white font=12 show use draw bold");
}
function mark(x,y,cat){
roiManager("Add");
j=roiManager("count");
roiManager("Select", j-1);
// concatenate the name
padded = toString(j/10000,4);
padded = substring(padded,2);
label = padded+"-"+cat;
roiManager("Rename", label);
run("Labels...", "color=white font=12 show use draw bold");
}
macro "Refresh [r]" {
run("Labels...", "color=white font=12 show use draw bold");
}
macro "Mark AVG [a]" {
cat = "AVG";
getCursorLoc(x, y, z, flags);
makePoint(x, y)
mark(x,y,cat);
}
macro "Mark SG [s]" {
cat = "SG";
getCursorLoc(x, y, z, flags);
makePoint(x, y)
mark(x,y,cat);
}
macro "Mark UnInf [d]" {
cat = "UnInf";
getCursorLoc(x, y, z, flags);
makePoint(x, y)
mark(x,y,cat);
}
macro "Mark Factory [f]" {
cat = "Factory";
getCursorLoc(x, y, z, flags);
makePoint(x, y)
mark(x,y,cat);
}
macro "toggle1 [1]" {
Stack.getActiveChannels(channels);
if (substring(channels,0,1)==1){
Stack.setActiveChannels("0"+substring(channels,1));
}
else {
Stack.setActiveChannels("1"+substring(channels,1));
}
}
macro "toggle2 [2]" {
Stack.getActiveChannels(channels);
if (substring(channels,1,2)==1){
Stack.setActiveChannels(substring(channels,0,1)+"0"+substring(channels,2));
}
else {
Stack.setActiveChannels(substring(channels,0,1)+"1"+substring(channels,2));
}
}
macro "toggle2 [3]" {
Stack.getActiveChannels(channels);
if (substring(channels,2,3)==1){
Stack.setActiveChannels(substring(channels,0,2)+"0"+substring(channels,3));
}
else {
Stack.setActiveChannels(substring(channels,0,2)+"1"+substring(channels,3));
}
}
macro "save roi and results [o]" {
saveAs("Results", "/Users/danrozelle/Desktop/Results.xls");
name=getTitle();
basename = substring(name,0,lengthOf(name)-4);
roiManager("Deselect");
roiManager("Save", "/Users/danrozelle/Desktop/"+basename+"_RoiSet.zip");
}
macro "Print Results [p]" {
setBatchMode(true);
name=getTitle();
basename = substring(name,0,lengthOf(name)-4);
roiManager("Deselect");
nROI = roiManager("count");
// add a new row and label it with this image name
setResult("image", nResults, basename)
for(i=0 ;i<nROI ;i++){
roiManager("Select", i);
label = call("ij.plugin.frame.RoiManager.getName", i);
cat = substring(label,5);
prev = getResult(cat, nResults-1);
if(prev>0){value = prev+1;}
else{value=1;}
setResult(cat, nResults-1, value);
}
if( getResult("AVG", nResults-1)>0 ){
AVGs = getResult("AVG", nResults-1);}
else {
setResult("AVG", nResults-1, 0);
AVGs = 0; }
if( getResult("SGs", nResults-1)>0 ){
AVGs = getResult("SG", nResults-1);}
else {
setResult("SG", nResults-1, 0);
SGs = 0; }
if( getResult("Factory", nResults-1)>0 ){
Factories = getResult("Factory", nResults-1);}
else {
setResult("Factory", nResults-1, 0);
Factories = 0; }
if( getResult("UnInf", nResults-1)>0 ){
Uninfected = getResult("UnInf", nResults-1);}
else {
setResult("UnInf", nResults-1, 0);
Uninfected = 0; }
// calculate %AVGs
setResult("n", nResults-1, AVGs+Factories+SGs+Uninfected);
setResult("Proportion AVGs", nResults-1, AVGs/(Factories+AVGs));
setResult("Proportion Infected Cells", nResults-1, (AVGs+Factories)/(AVGs+Factories+SGs+Uninfected) );
setBatchMode(false);
}