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

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
	<key>charactersArray</key>
	<array>
		<dict>
			<key>beginString</key>
			<string>'</string>
			<key>endString</key>

miura

//==============================================================================
//
// Project: EDF - Extended Depth of Focus
// 
// Author: Alex Prudencio (headless hack by Kota Miura and Christian Tischer, christian.tischer@embl.de)
// 
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Information: http://bigwww.epfl.ch/demo/edf/

miura

from fiji.threshold import Auto_Local_Threshold as ALT
from ij.gui import Roi
from imagescience.image import Image
from imagescience.feature import Laplacian
from process3d import Erode_, Dilate_, MinMaxMedian
from process3d import DistanceTransform3D as D3D
from Utilities import Counter3D
from ij.plugin import Thresholder, GaussianBlur3D, ZProjector, Duplicator
from ij.process import ImageProcessor

miura

from fiji.threshold import Auto_Local_Threshold as ALT
from ij.gui import Roi
from imagescience.image import Image
from imagescience.feature import Laplacian
from process3d import Erode_, Dilate_, MinMaxMedian
from process3d import DistanceTransform3D as D3D
from Utilities import Counter3D
from ij.plugin import Thresholder, GaussianBlur3D, ZProjector, Duplicator
from ij.process import ImageProcessor
import os, csv

miura

function onOpen() {
  var menuEntries = [ {name: "Create Diary Doc from Sheet", functionName: "createDocFromSheet"}];
  var ss = SpreadsheetApp.getActiveSpreadsheet();
  ss.addMenu("Fitness Diaries", menuEntries);
}

function createDocFromSheet(){
  var templateid = "1O4afl8SZmMxMFpAiN16VZIddJDaFdeRBbFyBtJvepwM"; // get template file id
  var FOLDER_NAME = "Fitness Diaries"; // folder name of where to put completed diaries
  // get the data from an individual user

miura

function onOpen() {
  var menuEntries = [ {name: "Create Diary Doc from Sheet", functionName: "createDocFromSheet"}];
  var ss = SpreadsheetApp.getActiveSpreadsheet();
  ss.addMenu("Fitness Diaries", menuEntries);
}

function createDocFromSheet(){
  var templateid = "1O4afl8SZmMxMFpAiN16VZIddJDaFdeRBbFyBtJvepwM"; // get template file id
  var FOLDER_NAME = "Fitness Diaries"; // folder name of where to put completed diaries
  // get the data from an individual user

miura

macro "Ratiometric FRET" {

  path    = getDirectory("Choose a Directory");
  list    = getFileList(path);
  length  = list.length;

  File.makeDirectory(path + "Imaging/");

  //FRET map creation