first commit: Mykola, a plugin to analyze beads ingestion by c-elegans worm

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+		http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>sc.fiji</groupId>
+        <artifactId>pom-fiji</artifactId>
+		<version>21.3.0</version>
+	</parent>
+
+	<groupId>BIIS.mpi-cbg</groupId>
+	<artifactId>Celegans_beads_analysis</artifactId>
+	<version>1.0.0</version>
+
+	<name>Celegans_beads_analysis</name>
+	
+	
+	<description>
+		a analysis plugin to measure the quantity of fluorescent Bead ingested by C-Elegans, worm are visualized in transmission
+	</description>
+
+	<dependencies>
+	
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>ij</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>fiji-lib</artifactId>
+		</dependency>
+		<dependency>
+  			<groupId>sc.fiji</groupId>
+  			<artifactId>Fiji_Plugins</artifactId>
+		</dependency>
+	</dependencies>
+
+
+	<developers>
+		<developer>
+			<id>developer_id</id>
+			<name> Benoit </name>
+			<email>ipf(A_T)mpi-cbg.de</email>
+			<organization>MPI-CBG</organization>
+			<roles>
+				<role>developer</role>
+			</roles>
+			<timezone>+1</timezone>
+		</developer>
+	</developers>
+
+	<repositories>
+		<!-- NB: for project parent -->
+		<repository>
+			<id>imagej.public</id>
+			<url>http://maven.imagej.net/content/groups/public</url>
+		</repository>
+	</repositories>
+
+	
+</project>

src/main/java/de/mpicbg/scf/cElegansBeadsAnalysis/Celegans_beads_analysis.java

+package de.mpicbg.scf.cElegansBeadsAnalysis;
+
+import ij.plugin.PlugIn;
+import ij.gui.GenericDialog;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.process.ImageProcessor;
+import ij.IJ;
+import ij.CompositeImage;
+import ij.plugin.filter.RankFilters;
+import ij.plugin.filter.GaussianBlur;
+import ij.plugin.ImageCalculator;
+import ij.process.ImageStatistics;
+
+/**
+ * This analysis was designed and implemented by Benoit Lombardot (MPI-CBG Scientific Computing facility)
+ * 
+ * Description:
+ * 
+ * Usage:
+ *  - To use the script open it in FIJI editor and run it after opening the image to analyse.
+ *  - Image should have 2 channels, one with a transmission image of the worm and one with an image of the fluorescent bids
+ * multiple timestep are processed as independent image
+ *  - The user will be requested to input: 
+ *      + the channel of the worm
+ *      + the channel of the beads
+ *      + the min area of region to keep in the worm mask
+ *      + the beads threshold type (manual or auto)
+ *  - The plugin will output: 
+ *      + an image of the worm mask
+ *      + an image of the bead selection on top of the beads image.
+ *      + 2 lines are appended to the results table indicating respectively the area and mean intensity
+ *      of the worm mask and the area and mean intensity of the beads selection
+ *  
+ */
+public class Celegans_beads_analysis implements PlugIn {
+
+	public int ch_bid, ch_tra, volMin, manual_thresh, R_bid_filt;
+	public boolean do_manual_thresh, do_bid_filt;
+	 
+	@Override
+	public void run(String arg) { 
+
+		if (showDialog()) {
+			ImagePlus imp_orig = IJ.getImage();
+			if (imp_orig != null)
+				process(imp_orig);
+		}		
+	}
+
+
+	public  boolean showDialog(){
+
+		GenericDialog gd = new GenericDialog("Process pixels");
+		gd.addNumericField("transmission channel",2, 0);
+		gd.addNumericField("bid channel", 1, 0);
+		gd.addNumericField("minimal mask area", 5000, 0);
+		gd.addCheckbox("use a manual threshold", false);
+		gd.addNumericField("manual bid threshold", 200, 0); 
+				
+		gd.showDialog();
+		if (gd.wasCanceled())
+			return false;
+
+		// get entered values
+		ch_tra = (int) gd.getNextNumber();
+		ch_bid = (int) gd.getNextNumber();
+		volMin = (int) gd.getNextNumber();
+		do_manual_thresh = gd.getNextBoolean();
+		manual_thresh = (int) gd.getNextNumber();
+		
+		return true;
+	}
+
+
+	public void process(ImagePlus imp_orig){
+
+		ImageStack stack = imp_orig.getImageStack();		
+		int Zslice = 1;
+		for( int frame=1; frame<=imp_orig.getNFrames(); frame++){
+		//for frame in range(5,6):
+			// extract the transmission image from the original stack
+			int stackIdx_tra = imp_orig.getStackIndex(ch_tra,Zslice,frame); // channel, slice, frame
+			ImageProcessor ip_tra_orig = stack.getProcessor(stackIdx_tra);
+			ImageProcessor ip_tra = ip_tra_orig.duplicate().convertToFloat();
+			ImagePlus imp = new ImagePlus("test",ip_tra);
+		
+			
+			// 1) top hat filtering ( I - open(I) ) of the transmission channel
+			int radius = 7;
+			ImageProcessor ip_tra_op = ip_tra.duplicate();
+			RankFilters filter = new RankFilters();
+			filter.rank(ip_tra_op, radius, RankFilters.MIN);
+			filter.rank(ip_tra_op, radius, RankFilters.MAX); // the two successive filter perfom an opening of the image
+			ImagePlus imp_bg = new ImagePlus("transmission bg", ip_tra_op);
+			ImageCalculator ImgCalc = new ImageCalculator();
+			ImagePlus imp_fg = ImgCalc.run("Subtract create", imp, imp_bg);
+
+		
+			// 2) gaussian conv of the foreground imp_fg
+			ImageProcessor ip_fg = imp_fg.getProcessor();
+			double sigma = 15.0;
+			GaussianBlur GBlur = new GaussianBlur();
+			GBlur.blurGaussian(ip_fg, sigma, sigma, 0.02);
+			
+		
+			// 3) define a threshold and make measure in the worm mask
+			IJ.setAutoThreshold(imp_fg, "Mean" );
+			IJ.run(imp_fg, "Convert to Mask", "");
+			IJ.run(imp_fg, "Invert", "");
+			IJ.run(imp_fg, "Analyze Particles...", "size="+volMin+"-Infinity show=Masks in_situ");
+			IJ.setThreshold(imp_fg, 1, 255  ); // set a threshold on the mask before doing the measurement
+			IJ.run("Set Measurements...","area mean limit redirect=None decimal=3");
+			
+			IJ.run(imp_fg, "Measure", "");
+
+			imp_fg.setTitle("Worms mask");
+			imp_fg.show();		
+		
+			// extract the bid image for the original image
+			int stackIdx_bid = imp_orig.getStackIndex(ch_bid,Zslice,frame); // channel, slice, frame;
+			ImageProcessor ip_bid = stack.getProcessor(stackIdx_bid);
+			ImagePlus imp_bid = new ImagePlus("bid image", ip_bid.duplicate() );
+
+
+			// filter bid image
+			ImagePlus imp_bid_fg = imp_bid.duplicate();
+
+			// thresold the beads image
+			ImageStatistics stats = ImageStatistics.getStatistics(imp_bid_fg.getProcessor(), ImageStatistics.MEAN | ImageStatistics.MIN_MAX , imp_bid.getCalibration()); 
+			double thresh_bid;
+			if( do_manual_thresh){ thresh_bid = manual_thresh;}
+			else{ thresh_bid = 3 * stats.mean; }
+			IJ.setThreshold(imp_bid_fg,thresh_bid,stats.max);
+			IJ.run(imp_bid_fg, "Convert to Mask", "");
+
+			// create the intersection of beads mask and worm masks
+			ImagePlus imp_bidMask = ImgCalc.run("AND create", imp_fg, imp_bid_fg);
+			
+			// create a selection of the mask to make measure on the original bid image
+			IJ.run(imp_bidMask, "Create Selection", "");
+			imp_bid = new ImagePlus("bid image", ip_bid.duplicate() );
+			imp_bid.setRoi(imp_bidMask.getRoi()); // apply the bid selection to the bid image 
+			IJ.run("Set Measurements...","area mean redirect=None decimal=3");
+			IJ.run(imp_bid, "Measure", "");
+		
+			// display an image illustrating the results
+			// original bid and transmission channel + the selection of the 
+			ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight() );
+			stack2.addSlice( ip_tra_orig );
+			stack2.addSlice( ip_bid);
+			
+			ImagePlus imp2 = new ImagePlus("result for frame " + frame , stack2);
+			imp2.setRoi(imp_bidMask.getRoi());
+			
+			int nChannels = 2;
+			int nSlices = 1;
+			int nFrames = 1;
+			imp2.setDimensions(nChannels, nSlices, nFrames);
+			CompositeImage comp = new CompositeImage(imp2, CompositeImage.COMPOSITE);
+			comp.show();
+		
+		}
+	}
+
+	
+	public static void main(final String... args)
+	{
+		new ij.ImageJ();
+		IJ.open("F:\\projects\\Mykola_Kurzchalia_paper review_walkin\\data\\Image 1.tif");
+		
+		
+		Celegans_beads_analysis analyzer = new Celegans_beads_analysis();
+		
+		analyzer.run("");
+		
+	}
+	
+}
\ No newline at end of file

src/main/resources/plugins.config

+# Name: Test_plugin
+# Author: BL
+# Version: 1.0.0
+
+# A single .jar file can contain multiple plugins, specified in separate lines.
+#
+# The format is: <menu>, "<menu label>", <class name>
+#
+# If something like ("<arg>") is appended to the class name, the setup() method
+# will get that as arg parameter; otherwise arg is simply the empty string.
+
+SCF>Mykola_19xx, "CElegans beads analysis", de.mpicbg.scf.cElegansBeadsAnalysis.Celegans_beads_analysis