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NewParamters_BugfixesProfilesOrientationVectorsBendingIndex
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New outputs: integrated intensity, average intensity on center line;
channel thresholds now also output in results for each cilium
Bugfixes: 1) output profiles were incorrect in v0.0.5 - sometimes the
profile points were not in consecutive order on cilium, resulting in
output zeros and wrong determination of bending index and orientation
vectors; 2) there was a bug in the basal stain detection at the ciliary
base and tip > fixed now.
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@hansenjn
hansenjn committed Feb 24, 2020
1 parent 0144b83 commit 172f828
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Showing 3 changed files with 282 additions and 189 deletions.
210 changes: 143 additions & 67 deletions src/main/java/ciliaQ_jnh/CiliaQMain.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
*
* Copyright (C) 2017-2020 Jan Niklas Hansen
* First version: June 30, 2017
* This Version: February 21, 2020
* This Version: February 24, 2020
*
* Parts of the code were inherited from MotiQ
* (https://github.com/hansenjn/MotiQ).
Expand Down Expand Up @@ -103,10 +103,10 @@ public class CiliaQMain implements PlugIn, Measurements {
double gXY = 2.0;
double gZ = 0.0;

boolean saveDate = true;
boolean saveDate = false;
boolean saveSingleCiliaTifs = false, saveSingleCilia3DImages = false, saveOverview3DImages = true;

String ChosenNumberFormat = "Germany (0,00...)";
String ChosenNumberFormat = nrFormats[0];

public void run(String arg) {
//&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
Expand All @@ -116,7 +116,7 @@ public void run(String arg) {
GenericDialog gd = new GenericDialog(PLUGINNAME + " - set parameters");
//show Dialog-----------------------------------------------------------------
//Note: .setInsets(top, left, bottom)
gd.setInsets(0,0,0); gd.addMessage(PLUGINNAME + ", Version " + PLUGINVERSION + ", \u00a9 2017 - 2019 JN Hansen", SuperHeadingFont);
gd.setInsets(0,0,0); gd.addMessage(PLUGINNAME + ", Version " + PLUGINVERSION + ", \u00a9 2017 - 2020 JN Hansen", SuperHeadingFont);
gd.setInsets(5,0,0); gd.addChoice("process ", taskVariant, selectedTaskVariant);

// gd.setInsets(10,0,0); gd.addMessage("Calibration", HeadingFont);
Expand Down Expand Up @@ -150,7 +150,7 @@ public void run(String arg) {
gd.setInsets(0,0,0); gd.addCheckbox("save result image for each individual cilium", saveSingleCiliaTifs);
gd.setInsets(0,0,0); gd.addCheckbox("save 3D visualizations for each individual cilium", saveSingleCilia3DImages);
gd.setInsets(0,0,0); gd.addCheckbox("save 3D visualizations for whole image", saveOverview3DImages);
gd.setInsets(0,0,0); gd.addChoice("output number format", nrFormats, nrFormats[1]);
gd.setInsets(0,0,0); gd.addChoice("output number format", nrFormats, nrFormats[0]);
gd.showDialog();
//show Dialog-----------------------------------------------------------------

Expand Down Expand Up @@ -438,20 +438,15 @@ public void windowClosing(WindowEvent winEvt) {
//Single-frame Mode
progress.notifyMessage("Single-timepoint workflow started...", ProgressDialog.LOG);
this.analyzeCiliaIn3DAndSaveResults(imp, measureC2local, measureC3local, measureBasalLocal, name[task], dir[task], startDate, filePrefix, subfolderPrefix);
}

//Get cilia data

/******************************************************************
*** OUPUT OPTIONS ***
*******************************************************************/

}
//Get cilia data and save them
processingDone = true;
break running;
}
progress.updateBarText("finished!");
progress.setBar(1.0);
progress.moveTask(task);
System.gc();
}
}

Expand Down Expand Up @@ -2055,7 +2050,7 @@ private void analyzeCiliaIn3DAndSaveResults(ImagePlus imp, boolean measureC2loca
maximumArcLength = cilia.get(i).arcLength[cilia.get(i).arcLength.length-1];
}
}
nrOfProfileCols = (int) Math.round(maximumArcLength / calibration);
nrOfProfileCols = (int) Math.round(maximumArcLength / calibration) + 1;
}

// SAVING
Expand Down Expand Up @@ -2152,29 +2147,41 @@ private void analyzeCiliaIn3DAndSaveResults(ImagePlus imp, boolean measureC2loca
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector y [" + calibrationDimension + "] (vector from first to last skeleton point)";
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector z [" + calibrationDimension + "] (vector from first to last skeleton point)";
appendTxt += " "; if(skeletonize) appendTxt += "cilia bending index (arc length of cilium / eucledian distance of first and last skeleton point)";

//profiles
if(measureC2local && skeletonize){
appendTxt += " " + "Profile A (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
appendTxt += " " + "Profile A (normalized to reconstruction channel) (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";

appendTxt += " "; if(measureC2local){appendTxt += "Intensity threshold A";}
appendTxt += " "; if(measureC3local){appendTxt += "Intensity threshold B";}
appendTxt += " "; if(measureBasalLocal){appendTxt += "Intensity threshold Basal Stain";}

appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Integrated A intensity";
appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Average A intensity on center line";
appendTxt += " "; if(skeletonize && measureC3local) appendTxt += "Integrated B intensity";
appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Average B intensity on center line";

if(skeletonize){
//profiles
if(measureC2local){
appendTxt += " " + "Profile A (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
appendTxt += " " + "Profile A (normalized to reconstruction channel) (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
}

if(measureC3local){
appendTxt += " " + "Profile B (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
appendTxt += " " + "Profile B (normalized to reconstruction channel) (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
}
}

if(measureC3local && skeletonize){
appendTxt += " " + "Profile B (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
appendTxt += " " + "Profile B (normalized to reconstruction channel) (arc length step: " + dformat6.format(calibration) + ")";
for(int i = 0; i < nrOfProfileCols-1; i++){
appendTxt += " ";
}
}


tw1.append(""+appendTxt);

Expand Down Expand Up @@ -2231,41 +2238,67 @@ private void analyzeCiliaIn3DAndSaveResults(ImagePlus imp, boolean measureC2loca
appendTxt += " "; if(cilia.get(i).sklAvailable){appendTxt += dformat6.format(cilia.get(i).orientationVector[2]);}
appendTxt += " "; if(cilia.get(i).sklAvailable){appendTxt += dformat6.format(cilia.get(i).bendingIndex);}

appendTxt += " "; if(measureC2local){appendTxt += dformat6.format(intensityThresholds[channelC2-1]);}
appendTxt += " "; if(measureC3local){appendTxt += dformat6.format(intensityThresholds[channelC3-1]);}
appendTxt += " "; if(measureBasalLocal){appendTxt += dformat6.format(intensityThresholds[basalStainC-1]);}

//profiles
if(skeletonize){
double [] iProfile;
double [] iProfileC2, iProfileC3;
if(measureC2local){
iProfileC2 = cilia.get(i).getIntensityProfile(2, calibration, false);
appendTxt += " ";
if(cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getSum(iProfileC2));
appendTxt += " ";
if(cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getAverage(iProfileC2));
}else{
iProfileC2 = new double [] {0.0};
appendTxt += " ";
appendTxt += " ";
}

if(measureC3local){
iProfileC3 = cilia.get(i).getIntensityProfile(3, calibration, false);
appendTxt += " ";
if(cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getSum(iProfileC3));
appendTxt += " ";
if(cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getAverage(iProfileC3));
}else{
iProfileC3 = new double [] {0.0};
appendTxt += " ";
appendTxt += " ";
}

if(measureC2local){
iProfile = cilia.get(i).getIntensityProfile(2, calibration, false);
if(iProfile != null){
if(iProfileC2 != null){
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilia.get(i).sklAvailable && j < iProfileC2.length){
appendTxt += dformat6.format(iProfileC2[j]);
}
}
iProfile = cilia.get(i).getIntensityProfile(2, calibration, true);
iProfileC2 = cilia.get(i).getIntensityProfile(2, calibration, true);
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilia.get(i).sklAvailable && j < iProfileC2.length){
appendTxt += dformat6.format(iProfileC2[j]);
}
}
}
}
if(measureC3local){
iProfile = cilia.get(i).getIntensityProfile(3, calibration, false);
if(iProfile != null){
if(iProfileC3 != null){
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilia.get(i).sklAvailable && j < iProfileC3.length){
appendTxt += dformat6.format(iProfileC3[j]);
}
}
iProfile = cilia.get(i).getIntensityProfile(3, calibration, true);
iProfileC3 = cilia.get(i).getIntensityProfile(3, calibration, true);
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilia.get(i).sklAvailable && j < iProfileC3.length){
appendTxt += dformat6.format(iProfileC3[j]);
}
}
}
Expand Down Expand Up @@ -2450,7 +2483,7 @@ private void analyzeCiliaIn4DAndSaveResults(ImagePlus imp, boolean measureC2loca
}
}
}
nrOfProfileCols = (int) Math.round(maximumArcLength / calibration);
nrOfProfileCols = (int) Math.round(maximumArcLength / calibration) + 1;
}

// SAVING
Expand Down Expand Up @@ -2520,6 +2553,10 @@ private void analyzeCiliaIn4DAndSaveResults(ImagePlus imp, boolean measureC2loca
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector y [" + calibrationDimension + "] (vector from first to last skeleton point) (time-averaged)";
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector z [" + calibrationDimension + "] (vector from first to last skeleton point) (time-averaged)";
appendTxt += " "; if(skeletonize) appendTxt += "cilia bending index (arc length of cilium / eucledian distance of first and last skeleton point) (time-averaged)";

appendTxt += " "; if(measureC2local){appendTxt += "Intensity threshold A";}
appendTxt += " "; if(measureC3local){appendTxt += "Intensity threshold B";}
appendTxt += " "; if(measureBasalLocal){appendTxt += "Intensity threshold Basal Stain";}

tw1.append(""+appendTxt);

Expand Down Expand Up @@ -2578,6 +2615,10 @@ private void analyzeCiliaIn4DAndSaveResults(ImagePlus imp, boolean measureC2loca
appendTxt += " "; if(timelapseCilia.get(i).sklAvailableInAllFrames){appendTxt += dformat6.format(timelapseCilia.get(i).orientationVectorAvg[2]);}
appendTxt += " "; if(timelapseCilia.get(i).sklAvailableInAllFrames){appendTxt += dformat6.format(timelapseCilia.get(i).bendingIndexAvg);}

appendTxt += " "; if(measureC2local){appendTxt += dformat6.format(intensityThresholds[channelC2-1]);}
appendTxt += " "; if(measureC3local){appendTxt += dformat6.format(intensityThresholds[channelC3-1]);}
appendTxt += " "; if(measureBasalLocal){appendTxt += dformat6.format(intensityThresholds[basalStainC-1]);}

//Averaged Profiles: TODO to be implemented
// double [] iProfile;
// if(measureC2local){
Expand Down Expand Up @@ -2768,7 +2809,16 @@ public void saveIndividualCiliumKinetics(TimelapseCilium cilium, String ciliumID
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector y [" + calibrationDimension + "] (vector from first to last skeleton point)";
appendTxt += " "; if(skeletonize) appendTxt += "orientation vector z [" + calibrationDimension + "] (vector from first to last skeleton point)";
appendTxt += " "; if(skeletonize) appendTxt += "cilia bending index (arc length of cilium / eucledian distance of first and last skeleton point)";


appendTxt += " "; if(measureC2local){appendTxt += "Intensity threshold A";}
appendTxt += " "; if(measureC3local){appendTxt += "Intensity threshold B";}
appendTxt += " "; if(measureBasalLocal){appendTxt += "Intensity threshold Basal Stain";}

appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Integrated A intensity";
appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Average A intensity on center line";
appendTxt += " "; if(skeletonize && measureC3local) appendTxt += "Integrated B intensity";
appendTxt += " "; if(skeletonize && measureC2local) appendTxt += "Average B intensity on center line";

//profiles
if(measureC2local && skeletonize){
appendTxt += " " + "Profile A (arc length step: " + dformat6.format(calibration) + ")";
Expand Down Expand Up @@ -2877,42 +2927,68 @@ public void saveIndividualCiliumKinetics(TimelapseCilium cilium, String ciliumID
appendTxt += " "; if(cilium.cilia.get(i).sklAvailable){appendTxt += dformat6.format(cilium.cilia.get(i).orientationVector[2]);}
appendTxt += " "; if(cilium.cilia.get(i).sklAvailable){appendTxt += dformat6.format(cilium.cilia.get(i).bendingIndex);}

appendTxt += " "; if(measureC2local){appendTxt += dformat6.format(intensityThresholds[channelC2-1]);}
appendTxt += " "; if(measureC3local){appendTxt += dformat6.format(intensityThresholds[channelC3-1]);}
appendTxt += " "; if(measureBasalLocal){appendTxt += dformat6.format(intensityThresholds[basalStainC-1]);}

//profiles
if(skeletonize){
progress.updateBarText("Determine intensity profiles for cilium " + ciliumID + " - time " + time);
double [] iProfile;
double [] iProfileC2, iProfileC3;
if(measureC2local){
iProfileC2 = cilium.cilia.get(i).getIntensityProfile(2, calibration, false);
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getSum(iProfileC2));
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getAverage(iProfileC2));
}else{
iProfileC2 = new double [] {0.0};
appendTxt += " ";
appendTxt += " ";
}

if(measureC3local){
iProfileC3 = cilium.cilia.get(i).getIntensityProfile(3, calibration, false);
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getSum(iProfileC3));
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable) appendTxt += dformat6.format(tools.getAverage(iProfileC3));
}else{
iProfileC3 = new double [] {0.0};
appendTxt += " ";
appendTxt += " ";
}

if(measureC2local){
iProfile = cilium.cilia.get(i).getIntensityProfile(2, calibration, false);
if(iProfile != null){
if(iProfileC2 != null){
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilium.cilia.get(i).sklAvailable && j < iProfileC2.length){
appendTxt += dformat6.format(iProfileC2[j]);
}
}
iProfile = cilium.cilia.get(i).getIntensityProfile(2, calibration, true);
iProfileC2 = cilium.cilia.get(i).getIntensityProfile(2, calibration, true);
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilium.cilia.get(i).sklAvailable && j < iProfileC2.length){
appendTxt += dformat6.format(iProfileC2[j]);
}
}
}
}
if(measureC3local){
iProfile = cilium.cilia.get(i).getIntensityProfile(3, calibration, false);
if(iProfile != null){
if(iProfileC3 != null){
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilium.cilia.get(i).sklAvailable && j < iProfileC3.length){
appendTxt += dformat6.format(iProfileC3[j]);
}
}
iProfile = cilium.cilia.get(i).getIntensityProfile(3, calibration, true);
iProfileC3 = cilium.cilia.get(i).getIntensityProfile(3, calibration, true);
for(int j = 0; j < nrOfProfileCols; j++){
appendTxt += " ";
if(cilium.cilia.get(i).sklAvailable && j < iProfile.length){
appendTxt += dformat6.format(iProfile[j]);
if(cilium.cilia.get(i).sklAvailable && j < iProfileC3.length){
appendTxt += dformat6.format(iProfileC3[j]);
}
}
}
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