lacan

run("Set Measurements...", "area mean standard modal min limit display redirect=None decimal=3");

run("Split Channels");
selectWindow("C1-Edu+_RFP+_(2).tif")
run("Median...", "radius=5");
setAutoThreshold("Li dark");
run("Create Selection");

selectWindow("C2-Edu+_RFP+_(2).tif");
run("Restore Selection");

lacan

/** 
 * Split Imaris Tracked Nuclei into separate ims files 
 * 
 * 
 * Author: Olivier Burri EPFL SV PTECH BIOP
 * for Noémie Chabot, Vastenhouw Lab
 * 
 * Last update: 01-10-2021
 * 
 * Dependencies: EasyXT https://github.com/BIOP

lacan

// Make 3D Shell and measure intensity at given thicknesses
// By Olivier Burri, EPFL - SV - PTECH - BIOP
// As a response to an ImageSC forum post: 
// https://forum.image.sc/t/help-with-shell-analysis-of-nuclei/54342
// Last update: 2021/07/23

raw = getTitle();

close("\\Others");

lacan

// This script was created for Anna Hamacher, as per an internal discussion on the ImageSC forum
// that stemmed from https://forum.image.sc/t/viewing-slide-scans-from-operetta-perkin-elmer-cls-as-overview-montage-images/52942/13?u=oburri
// Code by Olivier Burri, EPFL - SV - PTECH - BIOP
// Edited by Anna Hamacher
// Last edition: July 2022

#@ File dir (label="Images Folder", style="directory")
#@Integer downsample (label="Downsample Factor", value=1)
#@String z_projection_method (label = "Projection Type", choices = {"No Projection", "Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"} )
#@File outputDir (label="Output directory", style="directory")

lacan

print( "Your OMERO Server is Broken. Come back tomorrow" );

lacan

// Basic Template Matching using OpenCV with distance based NMS
// Author: Olivier Burri, EPFL - SV - PTECH - BIOP
// Inspiration: 
//  - https://docs.opencv.org/master/d4/dc6/tutorial_py_template_matching.html
//  - https://towardsdatascience.com/non-maximum-suppression-nms-93ce178e177c
// Date: 2021-05-25

def downsample = 10
def templateClass = "Template"
def detectedClass = "Detected"

lacan

// Action Bar description file :useful_shortcuts
// Provided by Olivier Burri for PCB-02
// Date: 20210420
// Copy this file (Do not rename it) to your Fiji installation under plugins/ActionBar
run("Action Bar","/plugins/ActionBar/useful_shortcuts.ijm");
exit();

<line>
<button> 1 line 1
label=Close All

lacan

#@ File xmlFolder (label="Folder with XML Files to combine", style="directory")

// List all XML Files
def files = xmlFolder.list({d, f-> f ==~ /.*.xml/ } as FilenameFilter).collect{ new File( xmlFolder, it) }

// Make a result folder
resultfolder = new File( xmlFolder, "combined")
resultfolder.mkdirs()

// Get the reference from which we will append the others to

lacan

/**
 * Macro to create concentric circles and sectors based on relative distance to an outer edge for a "donut-like" shape
 * 
 * Author: Olivier Burri, EPFL - SV - PTECH - BIOP
 * 
 * For Kailie Batsche, from a request on the Image.sc forum:
 * https://forum.image.sc/t/cross-sectional-analysis-cut-into-8-equal-sectors-with-three-concentric-rings/50302?u=oburri
 * 
 * Provided under GPL3
 * https://www.gnu.org/licenses/gpl-3.0.en.html

lacan

// Makes a montage with the selected settings from all open images
// By Olivier Burri, EPFL - SV - BIOP
// For Matjaz Panjan, Jožef Stefan Institute
// This needs the StackMontage plugin, which is available from the PTBIOP update site

def nRows = 2
def nCols = 1

// SCRIPT START