hirokai

# microjson - Minimal JSON parser/emitter for use in standalone scripts.
# No warranty. Free to use/modify as you see fit. Trades speed for compactness.
# Send ideas, bugs, simplifications to http://github.com/phensley
# Copyright (c) 2010 Patrick Hensley <[email protected]>

# std
import math
import StringIO
import types

hirokai

# auto_detect.py

from ij import IJ
from ij.plugin import ImageCalculator

IJ.run("Close All")
IJ.run("Stack From List...", "open=/Users/hiroyuki/Desktop/images.txt")
IJ.run("Gaussian Blur...", "sigma=5 stack")
imp = IJ.getImage()
imp.setTitle("all")

hirokai

# hiroutil.py

from ij import ImageStack, IJ


def load_stack(w,h,paths):
	stk = ImageStack(w,h)
	for path in paths:
		ip = IJ.openImage(path).getProcessor()
		stk.addSlice(ip)

hirokai

import Data.List
import Data.Monoid
import Text.Printf

data Sgn = Posi | Neg deriving Eq
data FP = FP Int Int Sgn | FPInt Int | FPDouble Double

add :: Double -> FP -> FP
add v (FPDouble a) = FPDouble (a + v)

hirokai

-- Generate NC files for PRODIA M45

module Main where

import Prelude
import Math hiding (log)

import Data.Array
import Data.Monoid
-- import Data.List (foldl)

hirokai

from ij import IJ
from ij.measure import ResultsTable
from ij.plugin.filter import ParticleAnalyzer
import time


def analyze(path):
	IJ.open(path)
	IJ.run("16-bit");
	IJ.run("Auto Threshold", "method=Minimum");

hirokai

# This script runs on Fiji.
# Just drag and drop this file into a Fiji window.

from ij import IJ, ImageStack, ImagePlus
from ij.process import ImageProcessor
from ij.plugin import ImageCalculator, ZProjector
from ij.plugin.filter import GaussianBlur, Analyzer, ParticleAnalyzer
from ij.measure import Measurements
import sys

hirokai

# This script runs on Fiji.
# Just drag and drop this file into a Fiji window.
# You can also use headless mode
# > /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless \
# > find_cells-headless.fiji.py /path/to/movie.avi

from ij import IJ, ImageStack, ImagePlus
from ij.process import ImageProcessor, ImageConverter
from ij.plugin import ImageCalculator, AVI_Reader, ZProjector, HyperStackConverter
from ij.plugin.filter import GaussianBlur, Analyzer, ParticleAnalyzer

hirokai

# Calculate trajectories using data from find_cells-headless.fiji.py

import csv
import sys


def norm_sq(a, b):
    return (a[0] - b[0]) ** 2 + (a[1] - b[1]) ** 2

hirokai

Cookbook for image processing in Julia

Image loading, showing, saving

using Images