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
#@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
#@String( label = "Selected frames (0 based, comma separated). Leave blank for all", required = false ) range_frames

NicoKiaru

 
// Modify the sequence of functions according to your need:
// - reImportAbbaRegions()
// - clearAllExcept(['Left: TH', 'Left: MB']) 
// - clearRight()
// - clearLeft()
//

reImportAbbaRegions() // Erase and re import regions

NicoKiaru

// To execute before:
// 0 - https://gist.github.com/NicoKiaru/723d8e628a3bb03902bb3f0f2f0fa466
// 1 - https://gist.github.com/NicoKiaru/f45f56e3ff2d1fb708821c110fbdee62

// save annotations
File directory = new File(buildFilePath(PROJECT_BASE_DIR,'export'));
directory.mkdirs();

def imageData = getCurrentImageData();
imageName = ServerTools.getDisplayableImageName(imageData.getServer())

NicoKiaru

/**
* ABBA Script : performs a cell detection on the root node annotation
* imported from ABBA and restores the child objects after the detection has been performed
* To use and modify like you need / want
* You need to have imported the regions before running this script. See https://gist.github.com/NicoKiaru/723d8e628a3bb03902bb3f0f2f0fa466 for instance
* See https://biop.github.io/ijp-imagetoatlas/
* Author: Olivier Burri, Nicolas Chiaruttini, BIOP, EPFL
* Date: 2022-01-26 
*/

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" )

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