romainGuiet

// BIOP Functions Library v1.0

/*
 * Returns the name of the parameters window, as we cannot use global variables, 
 * we just define a function that can act as a global variable
 */
function getWinTitle() {
    	win_title= toolName();
    	// If something is already open, keep it as-is.
	if(!isOpen(win_title)) {

romainGuiet

/*

************* Temporal-Color Coder *******************************
Color code the temporal changes.

Kota Miura (miura@embl.de)
Centre for Molecular and Cellular Imaging, EMBL Heidelberg, Germany

If you publish a paper using this macro, please acknowledge.

romainGuiet

/*
 * Use of the custom function rotateLine(...) 
 * Around a fixed point, get the x,y corrdinates 
 * of the points rotating around the Center at a defined distance
 * 
 */

selectWindow("blobs.gif");

// Center Point coordinates 

romainGuiet

title = getTitle;
close("\\Others");
roiManager("Reset");


sigma1 = newArray(1,2,3,4,5,10);
for (i = 0 ; i < lengthOf(sigma1) ; i++) {
	selectWindow(title);
	run("Duplicate...", "title=gb1");
	run("Gaussian Blur...", "sigma="+sigma1[i]);

romainGuiet

// ask user to select a folder
dir = getDirectory("Select A folder");
// get the list of files (& folders) in it
fileList = getFileList(dir);
// prepare a folder to output the images
output_dir = dir + File.separator + "output" + File.separator ;
File.makeDirectory(output_dir);


//activate batch mode

romainGuiet

roiManager("reset");

getStatistics(area, mean, min, max, std, histogram);

for (i = 1; i <= max; i++) {
	setThreshold(i, i);
	run("Create Selection");
	Roi.setName(IJ.pad(i,6))
	roiManager("Add");
}

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

romainGuiet

doAxialMeasure = true;


//get some informations about the image
image_Name = getTitle();
getDimensions(image_width, image_height, image_channels, image_slices, image_frames);
getVoxelSize(voxel_width, voxel_height, voxel_depth, voxel_unit);


doFWHM();

romainGuiet

import qupath.lib.scripting.*
import qupath.lib.regions.*
import qupath.lib.objects.* 
import qupath.lib.measurements.*
import qupath.lib.objects.hierarchy.PathObjectHierarchy
import qupath.lib.roi.*
  
import qupath.imagej.images.servers.*
import qupath.imagej.color.*
import qupath.imagej.gui.*

romainGuiet

archive_name = "models.zip"

import os
import zipfile 

# retrieve the pat of the current directory (bash command uses !...)
path=!pwd 
path = path[0] 

# create the archive path using path and archive_name