miura

importClass(Packages.ij3d.image3d.IntImage3D);
imp=IJ.getImage();
ima=new IntImage3D(imp.getStack());
r=3;
ima2=ima.createLocalMaximaImage(r,r,r, true);
plus=new ImagePlus("localmaxima",ima2.getStack());
plus.show();

miura

importClass(Packages.javax.media.j3d.VirtualUniverse);
vu = new VirtualUniverse();
if (vu == null)
      System.out.println("failed getting VirtualUniverse");
vuMap = vu.getProperties();
System.out.println("Java3D version: " + vuMap.get("j3d.version"));
System.out.println("Java3D vender: " + vuMap.get("j3d.vender"));
System.out.println("Java3D remderer: " + vuMap.get("j3d.renderer"))

miura

#!/bin/sh
for f in *.flv;
do
echo "Processing $f"
ffmpeg -i "$f" -target ntsc-dvd "${f%.flv}.mpg"
done

miura

// Shifts x position of signals in kymograph
// in respect to the drifts of egg edge position. 
// Kota Miura + Masa Mori
//
// duplicate image (for getting the edge shift)
// gaussian blurr (sigma = 1)
//threshould 

// registration in x direction
orgID = getImageID();

miura

//20120911
// Kota Miura
// Code fragments for registering two images
// & printing out shift in positions.
// refer to
// http://bigwww.epfl.ch/thevenaz/turboreg/turboRegMacro.txt
// for more examples. 

//using opened image opened and refering their title.

miura

var npos = 0; // this variable is better be global. 

macro "CCS_APP" {

    ipos = 1; // imaged position currently processed and "number of the file"
//    npos = 0; // number of total imaged positions
    ch = 0;   // channel, standardmäßig auf 0!
    frame = 0;
    slice = 0;
    noofcells = 4;  // needs to be loaded from segmenting algorithm.

miura

var npos = 0; // this variable is better be global. 
var directapply = 0; // "boolean" user input direct application of driftcorrect
var crop = 0;  // "boolean" user input crop to ROI 
var splitch = 0;  // "boolean" user input splitting of channels
var targetstack = 1 // ImageID of the stack that is to be processed 
var dir;
var cropxmax = 0;
var cropymax = 0;
var minout = 0;
var maxout = 0;

miura

# Simplest possible marimekko/mosaic plot

doInstall <- TRUE  # Change to FALSE if you don't want packages installed.
toInstall <- c("vcd", "ggplot2", "RColorBrewer")
if(doInstall){install.packages(toInstall, repos = "http://cran.us.r-project.org")}
lapply(toInstall, library, character.only = TRUE)

theme_set(theme_gray(base_size = 7))

# All you need to start with is individual count data, and a grouping variable

miura

File file = new File(path);

if (file.exists()) {
    ImagePlus image = IJ.openImage(file.getAbsolutePath());
    System.out.println(image.getTitle());
    ImagePlus[] split = ChannelSplitter.split(image);

    if (split != null) {
        System.out.println("SPLIT OK");
    } else {

miura

// This part taken from "for loop macro"
orgName = getTitle();
run("Split Channels");
c1 = "C1-" + orgName;
c2 = "C2-" + orgName;

//newly added
selectWindow(c1);
c1ID = getImageID(); 
selectWindow(c2);