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

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

// 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

// 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

/**
 * 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

/**
* 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

/* 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

#@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

/**
 * Simple script demoing how to check if an update site is enabled
 * and how to list all enabled update sites
 * 
 * @author Nicolas Chiaruttini
 * BIOP, EPFL, 2022
 **/ 

#@UpdateService updateService

NicoKiaru

/**
* Import regions from an ABBA registered project into QuPath
* See https://biop.github.io/ijp-imagetoatlas/
* Author: Olivier Burri, Nicolas Chiaruttini, BIOP, EPFL
* Date: 2022-01-26 
*/

// Erase and re import regions, the string should specify an existing key in the atlas ontology
// Available properties for Allen Brain Atlas are "acronym", "atlas_id", "color_hex_triplet", "graph_order", "hemisphere_id", "id", "name", "ontology_id", "parent_structure_id", "st_level"
importAbbaRegions( "acronym" )