ato

import java.io.IOException;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.attribute.BasicFileAttributes;

class TempDirectory {
    final Path path;

lacan

/*
 * Complex Format EXPORT MACRO
 * By Olivier Burri @ EPFL - SV - PTECH - BIOP
 * Given a folder, extracts all series inside all multi-file files with given extension in new folders 
 * Last edit: 13.02.2017
 */


 ////////////////////// SET PARAMETERS //////////////////////
 ////////////////////////////////////////////////////////////

GenevieveBuckley

"""Converting from ImagePlus to ImgPlus.
When an ImagePlus is made available by ImageJ 1.x, 
you can pass it to ImgLib2 as an Img via ImageJFunctions.wrap(imp)
http://javadoc.scijava.org/ImgLib2/net/imglib2/img/display/imagej/ImageJFunctions.html
"""
from ij import IJ
from net.imglib2.img import ImagePlusAdapter

image = IJ.openImage() # opens a file picker, or you can add the filename string as an argument.
output = ImagePlusAdapter.wrapImgPlus(image) #

romainGuiet

import ij.*
import ij.plugin.Duplicator
import ij.io.FileSaver

/**
 * 
 * Here is a groovy script which:
 * 	- Gets information about the current ImagePlus File (via imp.getOriginalFileInfo()),
 * 	- Retrieves its directory
 * 	- Creates an output subfolder

mutterer

// ImageJ macro to read 'timestamps' and 'events' from CZI files.

path = File.openDialog("Select CZI File");
s = File.openAsRawString(path, File.length(path));

o = indexOf(s,"CZTIMS");
o=o+0xcc;
n = parseInt(read32bAt(o));
timestamps = newArray(n);

romainGuiet

#@File(label="Please select an UserName-Lab", style="directory") selected_dir
#@String() projectName


/*
 * Macro to create a folder accordingly to BIOP template.
 * 
 * 
 * 
 * git need to be installed

lacan

/*
// ABOUT 
Exports Annotations for StarDist (Or other Deep Learning frameworks) 

// INPUTS
You need rectangular annotations that have classes "Training" and "Validation"
After you have placed these annotations, lock them and start drawing the objects inside

// OUTPUTS
----------

lacan

/**
 * Calculate 1D Full Width at half Maximum of a single line or a series of lines added to the ROI Manager
 * Created by Olivier Burri and Romain Guiet, BioImaging & Optics Platform (BIOP)
 * Last Update: 2020.10.21
 * 
 * Due to the simple nature of this code, no copyright applies
 *
 * Installation 
 * ------------
 * From within Fiji Please use "Plugins > Macros > Install" and select this file

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")

bogovicj

#@ UIService ui
#@ DatasetService ds

/*
 * Happy Pi Day 2022
 * 
 * This visualizes the bifurcation diagram for the "standard circle map"
 * https://en.wikipedia.org/wiki/Arnold_tongue#Standard_circle_map
 * 
 * (and its parameters are expressed in terms of pi)