NicoKiaru

#@ImageJ ij
#@Context ctx

// RISKY SCRIPT FOR THE HDD! RECOMMENDED TO TEST ON AN EMPTY USB STICK

def imp = IJ.openImage("http://imagej.nih.gov/ij/images/Spindly-GFP.zip");

File testExport = new File("F:/mitosis.ome.tiff");

NicoKiaru

/* Batch conversion of files to OME-TIFF following this install:
 * https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/ome-tiff-conversion/
 *  
 * Uses bioformats2raw and raw2ometiff
 * https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html
 *  
 * Works with MRXS files
 *
 * Nicolas BIOP, EPFL, 2021
 */

NicoKiaru

/**
* Example of generative image (here a recursive Fiji logo) displayed in BigDataViewer
* The PTBIOP update site needs to be enabled
*/

import bdv.util.Procedural3DImageShort
import net.imglib2.RealRandomAccessible
import bdv.util.BdvFunctions
import bdv.util.BdvOptions
import bdv.util.BdvHandle

NicoKiaru

/**
 * BIOP, EPFL, Nicolas Chiaruttini, 18th April 2021
 * Simple script for a simple registration test
 */

import ij.IJ
import ch.epfl.biop.wrappers.elastix.ij2commands.Elastix_Register
import ch.epfl.biop.wrappers.transformix.ij2commands.Transformix_TransformImgPlus
import ij.gui.WaitForUserDialog

NicoKiaru

// You need to activate https://biop.epfl.ch/Fiji-Bdv-Playground/  for this script to function
// It takes a Nikon ND2 file and batch exports individual series, optionally Z Projected and rescaled
// Nicolas Chiaruttini, BIOP, EPFL, 2021

#@CommandService cs

#@SourceAndConverterService sac_service

#@File(label="Select your Nikon ND2 file (single timepoint only)", style="open") nikonNd2File
#@File(label="Select directory to save images", style="directory", value="default") saveDir

NicoKiaru

// You need to activate https://biop.epfl.ch/Fiji-Bdv-Playground/  for this script to function
// It takes a Nikon ND2 file and Visualizes it lazily in BigDataViewer, also opens some windows to control Brightness
// Of each channel present in the file
// Nicolas Chiaruttini, BIOP, EPFL, 2021

#@CommandService cs

#@SourceAndConverterService sac_service

#@File(label="Select your Nikon ND2 file (single timepoint only)", style="open") nikonNd2File

NicoKiaru

package ch.epfl.biop.trackmategdsc;

import fiji.plugin.trackmate.*;
import fiji.plugin.trackmate.action.AbstractTMAction;
import fiji.plugin.trackmate.action.ExportTracksToXML;
import fiji.plugin.trackmate.action.TrackMateAction;
import fiji.plugin.trackmate.action.TrackMateActionFactory;
import fiji.plugin.trackmate.gui.TrackMateGUIController;
import fiji.plugin.trackmate.util.TMUtils;
import org.jdom2.Element;

NicoKiaru

/**
 * Dendrite Info Display and Analysis
 * PTBIOP update site should be enable
 * NeuroMorpho update site should be enabled
 * 
 * This script takes a dendrite image as an input and a SNT traces files where:
 * - Spine branch should be tagged 'Spine' (at least)
 * - The branches on which tagged spines are located should be tagged 'root'
 * 
 * The script outputs:

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

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