I am sorry if I make a mess, the only programming experience I have is starting a short bioinformatics Python course, so I hope I don't get bashed and I kindly ask for help. I have been using a script for ImageJ written by someone else and the script is basically selecting cells and measuring the intensity of fluorescence, which is later used to compare data between various experiments, all part of neuroscience. I had no troubles until recently, but I think that after an update of ImageJ something is not going right. I haven't changed the way I work or anything. This is my first post here, I hope I tagged it right and I don't cause any inconvenience. Of course I hope for helpful answers and I will be grateful for any advice. Should I be worried or should I just continue with the work? After I get the solid basics of Python I will probably learn Java. I intend to use it for research purposes, neuroscience to be specific. If someone also has a better idea for this kind of work (selecting cells and measuring the intensity of fluorescence in two different channels) then I would also be grateful. So, hello all and here is the output when I load the script:
(Fiji Is Just) ImageJ 2.0.0-rc-36/1.50a; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 941MB of 6023MB (15%)
java.lang.Error: Error: could not match input
at net.imagej.ui.swing.script.highliters.ImageJMacroTokenMaker.zzScanError(ImageJMacroTokenMaker.java:2619)
at net.imagej.ui.swing.script.highliters.ImageJMacroTokenMaker.yylex(ImageJMacroTokenMaker.java:2882)
at net.imagej.ui.swing.script.highliters.ImageJMacroTokenMaker.getTokenList(ImageJMacroTokenMaker.java:2469)
at org.fife.ui.rsyntaxtextarea.TokenMakerBase.getLastTokenTypeOnLine(TokenMakerBase.java:219)
at org.fife.ui.rsyntaxtextarea.RSyntaxDocument.updateSyntaxHighlightingInformation(RSyntaxDocument.java:646)
at org.fife.ui.rsyntaxtextarea.RSyntaxDocument.setSyntaxStyle(RSyntaxDocument.java:530)
at org.fife.ui.rsyntaxtextarea.RSyntaxTextArea.setSyntaxEditingStyle(RSyntaxTextArea.java:2764)
at net.imagej.ui.swing.script.EditorPane.setLanguage(EditorPane.java:490)
at net.imagej.ui.swing.script.EditorPane.setLanguage(EditorPane.java:435)
at net.imagej.ui.swing.script.EditorPane.setLanguageByFileName(EditorPane.java:423)
at net.imagej.ui.swing.script.EditorPane.setFileName(EditorPane.java:369)
at net.imagej.ui.swing.script.TextEditor.setEditorPaneFileName(TextEditor.java:1683)
at net.imagej.ui.swing.script.TextEditor.open(TextEditor.java:1388)
at net.imagej.legacy.plugin.DefaultLegacyEditor.open(DefaultLegacyEditor.java:93)
at net.imagej.legacy.DefaultLegacyHooks.openInEditor(DefaultLegacyHooks.java:299)
at ij.io.Opener.open(Opener.java)
at ij.io.Opener.openAndAddToRecent(Opener.java:288)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:662)
And the code I have, in case it is needed:
Variable initiation
**********************************************
*/
// Arrays
var list = newArray();
// Strings and numbers
var dir = ""; // directory
var outDir = ""; // output directory
var index = 0; // Index of folder (well)
var minSize = 80, maxSize = 20000; // min and max size of nuclei for segmentation (in pixels)
var minCirc = 0;
var valueStop = 0;
var valueStart = 0;
var startSlice=1; // starts at slice 1, if some slices are done aldready, this value can be increased
var newrun = 1;//has to be 1!!!!
var n=0;
/*
**********************************************
Signal Measurements
**********************************************
*/
macro "[M] Measure Nuclear Foldings"
{
setup();
setBatchMode(false);
print("Analysis");
print("************************************************************");
index = 0;
for(j=0; j<list.length; j++)
{
path = dir + list[j];
if(endsWith(path,'1.tif'))
{
open(path);
print(list[j],"list");
print("list");
id = getImageID;
title = getTitle();
slices=nSlices;
print(n);
prefixCh2 = replace(title,"1.tif","2.tif");
path2 = dir + prefixCh2;
open(path2);
idch2 = getImageID;
for(ii=startSlice; ii<slices+1; ii++)
{
//run("Collect Garbage");
selectImage(id);
if(newrun==1)
{
newrun=2;
run("Out [-]");
run("Out [-]");
//get a duplicate to present the rois and to measure the true values
//this copy has to have multiple slices so the roimanager can add the
//slice number to the results table
selectImage(id);
setSlice(ii);
run("Duplicate...", "title=DuplicateChannel1.tif duplicate range="+1+"-"+slices);
id2 = getImageID;
run("Out [-]");
run("Out [-]");
selectImage(idch2);
run("Out [-]");
run("Out [-]");
}
selectImage(idch2);
setSlice(ii);
//get a duplicate of a single image on which you will do the cell detection
selectImage(id);
setSlice(ii);
run("Duplicate...", "title=BLUEchannel.tif");
BLUEid = getImageID;
selectImage(BLUEid);
run("Out [-]");
roiManager("reset");
run("Gaussian Blur...", "sigma=2");
setAutoThreshold("Triangle");
run("Convert to Mask");
run("Gaussian Blur...", "sigma=2");
setAutoThreshold("Li"+" dark");
run("Analyze Particles...", "size="+60+"-"+6000+" circularity="+0+"-1.00 show=Nothing add stack");
n=roiManager("count");
print(n);
selectImage(BLUEid);
close;
selectImage(idch2);
roiManager("deselect");
roiManager("Show All");
roiManager("Set Color", "red");
if(n>0)
{
selectImage(id2);
setSlice(ii);
roiManager("deselect");
roiManager("measure");
selectWindow("Results");
//start removing Rois that are incorrect
if (nImages==0) exit("There is no image open");
if (!isOpen("ROI Manager")) exit("There is no ROI manager open");
if (!isOpen("Results")) exit("There is no results table. Create via Multi Measure option in ROI Manager");
if (roiManager("count")==0) exit("There are no ROIs loaded in the ROI manager");
roiManager("Associate", "true");
roiManager("Centered", "false");
roiManager("UseNames", "true");
setTool("rectangle");
roiManager("Show All with labels");
roiManager("Show All");
roiManager("Deselect");
leftButton=16;
x2=-1; y2=-1; z2=-1; flags2=-1;
logOpened = false;
print("Close this window when finished");
while (!logOpened || isOpen("Log")) {
§ getCursorLoc(x, y, z, flags);
if (x!=x2 || y!=y2 || z!=z2 || flags!=flags2) { // Only when mouse moves new locatation is logged
wait(20); // Might have to be increased with large number of ROIs
if (flags&leftButton!=0) {
// Check that a ROI is selected
if (roiManager("index")!=-1){
RoiName= Roi.getName();
print(RoiName);
del = false; // Becomes "true" when a result is deleted from the table
selectWindow("Results");
valueDiff = (roiManager("count"));
valueStop=valueStart+valueDiff;
for (i=valueStart;i<valueStop;i++){
if (del==false){
// Check label ROI against labels in Results table
S = getResultLabel(i);
if (matches(S,".*"+RoiName+".*")){
selectWindow("Results");
IJ.deleteRows(i, i);
del = true;
}
}
}
roiManager("Delete");
}
logOpened = true;
}
x2=x; y2=y; z2=z; flags2=flags; // Only when mouse moves new location is logged
wait(10);
// Takes care that one mouse click is recorded as one mouse click
}
}
}
//keep track of the index of the results tabel, this increases now
valueRois = (roiManager("count"));
valueStartOld=valueStart;
valueStart = valueStartOld+valueRois*2;
//add something to change to channel two and measure the values of these cells.
if(n>0)
{
selectImage(idch2);
setSlice(ii);
roiManager("deselect");
roiManager("measure");
selectWindow("Results");
saveAs("Measurements",dir+"ResultsFinalDanaiCh1.txt");
}
/*
selectImage(id2);
setSlice(ii);
run("Duplicate...", "title=duplicateID2.tif");
id3 = getImageID;
selectImage(id3);
run("Out [-]");
roiManager("Show All");
roiManager("Set Color", "red");
saveAs("tif",dir+ii+"Channel1_image.tif");
selectImage(id3);
close;
*/
}
}
}
print("************************************************************");
}
/*
**********************************************
Functions
**********************************************
*/
function getMoment()
{
MonthNames = newArray("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec");
DayNames = newArray("Sun", "Mon","Tue","Wed","Thu","Fri","Sat");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
TimeString ="Date: "+DayNames[dayOfWeek]+" ";
if (dayOfMonth<10) {TimeString = TimeString+"0";}
TimeString = TimeString+dayOfMonth+"-"+MonthNames[month]+"-"+year+"\nTime: ";
if (hour<10) {TimeString = TimeString+"0";}
TimeString = TimeString+hour+":";
if (minute<10) {TimeString = TimeString+"0";}
TimeString = TimeString+minute+":";
if (second<10) {TimeString = TimeString+"0";}
TimeString = TimeString+second;
return TimeString;
}
function setup()
{
print("\\Clear");
run("Close All");
run("Clear Results");
roiManager("reset");
//run("Collect Garbage");
run("Colors...", "foreground=white background=black selection=yellow");
setOption("BlackBackground", false);
run("Set Measurements...", "area mean shape stack slices ii center of mass display redirect=None decimal=4");
dir = getDirectory("");
list = getFileList(dir);
isWin=indexOf(getInfo("os.name"),"Windows")>=0;
//if(isWin)outDir=dir+"Output\\";
//else outDir=dir+"Output/";
//if(!File.exists(outDir))File.makeDirectory(outDir);
TimeString = getMoment();
print(TimeString);
print("************************************************************");
}
§character in the middle of your code that I believe does not belong there. - Jan Eglinger