hirokai

# Example of Fiji script for batch processing.

import csv


# Stub
# You can put whatever opearations you want to apply.
def get_radialprofile(imp, cx, cy, r, num_bin)
    return None

hirokai

# Example of Fiji script for calculating a radial profile.

from ij import IJ
from ij.process import ImageStatistics as IS
from ij.gui import Roi, OvalRoi


# Get mean pixel intensity in a specified donut-shaped area
def get_mean_in_donut(imp, cx, cy, min_r, max_r):
    options = IS.MEAN | IS.MEDIAN | IS.MIN_MAX | IS.AREA

hirokai

• Source code in the tutorial
  • Working examples
    • Image statistics
    • Radial profile
    • Nanodot spacing analysis
      • server written in Haskell language
    • Batch processing with a csv file
• Resources
  • Image processing
• Principles of Digital Image Processing

hirokai

from ij import IJ, ImagePlus, ImageStack, WindowManager

from ij.plugin import ContrastEnhancer,StackCombiner,ImageCalculator
from ij.process import ImageConverter, ImageProcessor
from time import sleep
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141103/05-A FC4 488 568/"

hirokai

from ij import IJ, ImagePlus, ImageStack
from ij.process import ColorProcessor, ImageConverter
from ij.plugin import ContrastEnhancer, ImageCalculator, StackCombiner
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141126 Immunostaining/"


def in_path(folder,num):
	return [folder + "01 FC4 of 1125/02 tirf and confocal/tirf_"+row[0]+"/Pos0/img_000000000_488tirf_100x_000.tif",

hirokai

from ij import IJ,ImagePlus
from ij.process import ColorProcessor
from ij.plugin import ContrastEnhancer
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141126 Immunostaining/"

def crop(imp,x,y,w,h):
    imp.setRoi(x,y,w,h)
    st = imp.getStack()

hirokai

run("Enhance Contrast", "saturated=0.35");
run("Gaussian Blur...", "sigma=5");
run("8-bit");
run("Auto Local Threshold", "method=Mean radius=50 parameter_1=0 parameter_2=0 white");
run("Invert");
run("Fill Holes");
run("Watershed");
run("Set Measurements...", "area mean standard modal min center bounding redirect=None decimal=2");
run("Analyze Particles...", "size=150-300 show=Ellipses display clear include");

hirokai

from math import cos, sin, pi, sqrt, atan
import matplotlib.pyplot as plt
import numpy as np
from mydata import *

# vector addition


def abs2(a):
	return a[0] * a[0] + a[1] * a[1]

hirokai

# 02A: Make time lapse of stitched image.

from ij import IJ, ImagePlus, ImageStack, WindowManager

from ij.plugin import ContrastEnhancer,StackCombiner,ImageCalculator
from ij.process import ImageConverter, ImageProcessor
from java.awt.image import IndexColorModel
from time import sleep
import csv
from jarray import zeros

hirokai

#!/usr/bin/env ruby

# Collecting elapsed time from all frames and positions.

require 'csv'

positions = [["4-Pos_000_000", "4-Pos_000_001", "4-Pos_000_002", "4-Pos_000_003"], ["4-Pos_001_000", "4-Pos_001_001", "4-Pos_001_002", "4-Pos_001_003"],
				["4-Pos_002_000", "4-Pos_002_001", "4-Pos_002_002", "4-Pos_002_003"], ["4-Pos_003_000", "4-Pos_003_001", "4-Pos_003_002", "4-Pos_003_003"]]

CSV.open("02B frames.csv", "wb") do |csv|