ekatrukha

clear all

%% READ IMAGE FROM FILE

I=imread('kymo.bmp');

%maximum delay time (in frames)
nMaxTime = 60;

ekatrukha

var system;
var input, button, greeting;
var diffusion;
var nParticleTotN;
var sigma;
var nLifetime;
var velocityx;
var velocityy;

function setup() {

ekatrukha

//ImageJ macro making a movie (stack) of zooming on selected rectangle (ROI)
//Eugene Katrukha katpyxa at gmail.com
requires("1.48h");

//check if there is rectangular selection
if(selectionType() ==0)
{
	sTitle=getTitle();
	sMovieTitle=sTitle+"_zoom_movie";
	setBatchMode(true);

ekatrukha

/*

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

Kota Miura ([email protected])
Centre for Molecular and Cellular Imaging, EMBL Heidelberg, Germany

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

ekatrukha

//ImageJ macro making a tilted movie out of stack
//uses shear transform + rotation
//Eugene Katrukha katpyxa at gmail.com
requires("1.48h");

sTitle=getTitle();
sMovieTitle=sTitle+"_tilt_movie";
setBatchMode(true);

//Dialog

ekatrukha

//get folder with files
input = getDirectory("Input directory");

//!!!define suffix of files here
suffix = ".tif";

list = getFileList(input);
for (i = 0; i < list.length; i++) 

ekatrukha

import sys
from math import pi
from math import sqrt
from random import shuffle

from java.awt import Color

from ij import WindowManager
from ij.measure import ResultsTable
from ij.plugin.frame import RoiManager

ekatrukha

// Providing an image and polyline, macro illustrates
// (creates a stack with animation)
// "Straighten" ROI function of ImageJ
// 2021.01.28 Eugene Katrukha / katpyxa at gmail dot com

if (nImages<1)
{
	exit("This macro needs an input image. Open something");
}
if(selectionType()!=6)

ekatrukha

inputFileName= 'wt chm';

dtin=importdata(strcat(inputFileName,'.csv'));
dBinMin=0;
dBinMax=6;
dBin = 0.1;

%first values then weights
dt=horzcat(dtin(:,2),dtin(:,1));

ekatrukha

//script needs 2 ROIs to be present in the ROI manager
//+ image itself
//+ Results table with particle coordinates
// First ROI is an outline of the cell (FREEHAND selection)
// The second ROI is a Point ROI of the cell's center
// Partice/vesicles coordinates colum names in Results table
// should start with X,Y 

origID=getImageID();
getPixelSize(unit,pxW,pxH);