NicoKiaru

// Open a URL from OMERO with caching into Fiji as an ImagePlus
// Requires PTBIOP and OMERO 5.5 5.6 update site
// Written by Nicolas Chiaruttini on 24th Jan 2025
// Try https://omero-tim.gerbi-gmb.de/webclient/?show=image-104300 with:
// login: read-tim
// passwd: read-tim

#@CommandService cs
#@String(label="omero url") url
#@SourceAndConverterService source_service

NicoKiaru

/**
 * This script takes a 3D input a stack with beads and a stack of the same size
 * with single points placed at the center of detected beads / spots
 * this is the second step to compute a clean PSF with distillation.
 * 
 * Example for this script:
 * - Image = https://zenodo.org/records/14203207/files/30x1000_FS-025_FW-60_AC-170.tif
 * - Bead Image = the result of the DetectBeads script
 * 
 * Link to useful threads:

NicoKiaru

/**
 * This script takes a 3D input a stack with beads and will output a stack of the same size
 * with single points placed at the center of detected beads / spots
 * this is the first step to compute a clean PSF with distillation.
 * 
 * The rest of the PSF computation happens in the script ExtractPSF
 * 
 * For detecting beads in 3D the method used is the Laplacian of Gaussian detector by Trackmate which has 2 parameters
 * It can be useful to use the TrackMate GUI before using this script in order to check which parameters to use.
 * 

NicoKiaru

#@File f

IFormatReader r = new ImageReader();
IMetadata meta = MetadataTools.createOMEXMLMetadata();
r.setMetadataStore(meta)
r.setId(f.getAbsolutePath());
meta = (IMetadata) r.getMetadataStore(); // Retrieves the metadata object
int nImages = r.getSeriesCount(); // Number of images within the file
for (int iImage = 0; iImage<nImages; iImage++) {
	r.setSeries(iImage);

NicoKiaru

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