NicoKiaru

/**
 * A small theory about pile-up effect in FLIM - unfortunately I lost the way I made these equations
 * 
 * (I think the documentation below is wrong: what is n ? what is alpha ? why are they not the same ?)
 * 
 * Here, we model a poisson process for the number of photon emitted per excitation pulse. (parameter alpha)
 * In other words: alpha is the parameter of the poisson distribution ( = average number of photons emitted after an excitation pulse)
 * 
 * And each photon has a mono-exponential lifetime tau
 * 

NicoKiaru

package loci.formats.in.libczi;

import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import java.util.ArrayList;

import loci.common.DataTools;
import ome.units.UNITS;
import ome.units.quantity.Length;

NicoKiaru

#@ImagePlus structural_images

#@ImagePlus label_image

#@Double atlas_precision_mm

#@ObjectService os

NicoKiaru

/**
 *  Makes a big 2d procedural plane and saves it as a multiresolution ome.tiff image
 *  
 *  Tested on a 128 000 x 128 000 images with 8000 objects (11G pix), 10 resolutions levels, downscale 2 ~ 30 minutes to generate
 *  
 *  PTBIOP update site needed
 *  @author Nicolas Chiaruttini, 2023
 */

#@Integer nPixelsX

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

package ch.epfl.biop.test;

/**
 * Simple tests of potential arithmetic simplification that I think
 * a JIT compiler should be able to do:
 * - Multiplications by ones
 * - Additions with zeros...
 *
 * My wish is that special cases matrices computations could be auto-simplified.
 * (a translation matrix is only 3 additions in 3D)

NicoKiaru

// See https://forum.image.sc/t/reconstructing-tomographic-light-sheet-data-2d-slice-into-cylindrical-3d-volume
// Bigdataviewer-playground update site need to be activated

#@ConvertService cs
#@ImagePlus(required=false) image
#@int numberOfAngles
#@BdvHandle(required=false) bdvPolar
#@BdvHandle(required=false) bdvCar
#@ColorRGB color
#@SourceAndConverterBdvDisplayService bdvDisplay 

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

#@File(label = "Select the 'Images' folder of your Operetta dataset", style = "directory") folder
#@TaskService taskService


def task = taskService.createTask("Operetta Sanitizer ")

try {
	task.setStatusMessage("Listing files...")
	task.setProgressMaximum(0)
	def fileList = folder.list() as List

NicoKiaru

// You need to activate https://biop.epfl.ch/Fiji-Bdv-Playground/  for this script to function
// It takes a file and batch exports individual series, optionally Z Projected and rescaled
// Deals pretty correctly with Big dataset + saves multiresolution OME-TIFFs file, keeping the positional metadata
// Nicolas Chiaruttini, BIOP, EPFL, 2022

#@File(label="Dataset") image_file
#@boolean(label="Show advanced opening parameters") advanced
#@String(label="Give a name to your dataset") dataset_name
#@String( label = "Select a subset of channels (0 based, comma separated). Leave blank for all", value="") range_channels
#@String( label = "Selected slices (0 based, comma separated). Leave blank for all", required = false ) range_slices