NicoKiaru

import org.scijava.command.Command;
import org.scijava.command.DynamicCommand;
import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import ij.ImagePlus;
import net.imagej.ImageJ;

@Plugin(type = Command.class, menuPath = "Plugins>MyCommand>Say Hello")
public class CmdTest extends DynamicCommand{

NicoKiaru

#@ImagePlus imp

import ij.ImagePlus;
import ij.gui.Roi;
import java.util.HashSet;
import ij.process.ImageProcessor;
import ij.plugin.filter.ThresholdToSelection;
import ij.plugin.frame.RoiManager;
import ij.process.FloatProcessor

NicoKiaru

/**
 *  GROOVY SCRIPT COMPUTING ON THE FLY EDGES OF A LABEL IMAGE
 *  -----
 * 	 - Computes a sample label image
 *   - Computes lazily with a disk cached cell img an image which finds the border of the labels in 3D
 *   - Displays both images in BigDataViewer
 *
 *  Code to create the label image mainly copied from:
 *  - https://imagej.net/ImgLib2_Examples#Example_8_-_Working_with_sparse_data
 *  - And https://github.com/imglib/imglib2-cache-examples

NicoKiaru

import net.imagej.ops.OpUtils
opsByNS = [:]
#@ImageJ ij

ij.op().ops().each{op ->
  ns = OpUtils.getNamespace(op)
  name = OpUtils.stripNamespace(op)
  if (!opsByNS.containsKey(ns)) {

NicoKiaru

import ch.epfl.biop.bdv.bioformats.command.OpenFilesWithBigdataviewerBioformatsBridgeCommand
import ch.epfl.biop.bdv.bioformats.command.BioformatsBigdataviewerBridgeDatasetCommand
import sc.fiji.bdvpg.services.SourceAndConverterServices
import bdv.viewer.SourceAndConverter
import ij.gui.WaitForUserDialog
import ch.epfl.biop.scijava.command.BdvViewToImagePlusExportCommand
import sc.fiji.bdvpg.scijava.command.bdv.BdvSourcesAdderCommand


/**

NicoKiaru

#@ImagePlus stack
#@Integer(label = "Channel DAPI") chDAPI = 1
//Integer(label = "Channel Cytoplasm") chCyto = 3
#@Integer(label = "Channel Measured") chAnalyzed = 2
#@Integer(label = "Nucleus Enlargement in Pixel") enlarge_nucleus_px = 30
#@Boolean(label = "Load Previous ROIS") loadPreviousRois = false
#@Boolean(label = "Save ROIS") saveDetectedRois = false
#@Boolean(label = "Erase previously existing ROIS") erase = false
#@Boolean(label = "Test mode") testMode = false

NicoKiaru

/**
 * Diana analysis for Selene :
 * Requirements:
 * - An image which contains associated ROIs for nuclei and cytoplasm
 * - ROI names should follow the pattern:
 *     - Cyto_#index_of_cell < Cytoplasm ROI
 *     - Nucleus_#index_of_cell < Nucleus ROI
 *     so Cyto_0, Nucleus_0, Cyto_1, Nucleus_1, ...
 *     
 * - DiAna plugin installed (follow instructions https://imagejdocu.tudor.lu/plugin/analysis/distance_analysis_diana_2d_3d/start)

NicoKiaru

import net.imglib2.position.FunctionRandomAccessible
import net.imglib2.type.numeric.integer.UnsignedShortType
import java.util.function.BiConsumer
import bdv.util.BdvFunctions
import bdv.util.BdvOptions
import net.imglib2.FinalInterval
import net.imglib2.view.Views
import net.imglib2.realtransform.AffineTransform3D
import net.imglib2.type.numeric.ARGBType

NicoKiaru

/**
 * Allows to visualize the rois of a RoiManager linked to an ImagePlus
 * into bigdataviewer.
 * 
 * REQUIREMENT : install the bigdataviewer-playground update site ( still in development! expect things to break!! )
 * Update site : https://biop.epfl.ch/Fiji-Bdv-Playground/
 * Source code : https://github.com/bigdataviewer/bigdataviewer-playground
 * 
 * 
 * A lazy image is generated which display a small square region around each ROI

NicoKiaru

/**
 * Allows to compute in a simple manner different regions of a lifetime stack image
 *
 * REQUIREMENT : For Picoquant file reading, install PTU-Reader (https://github.com/ekatrukha/PTU_Reader)
 * 
 * How to use the script:
 * 0 open a PTU file
 * 1 make regions of interest and store them into the ROI Manager
 * 2 select the lifetime stack
 * 3 execute the script and provide the necessary parameters