hirokai

# tools_fiji.py

from ij import ImagePlus, ImageStack, IJ

print('tools_fiji.py loaded.')


# Image load/save

# Open a list of files.

hirokai

#!/usr/bin/env python

import matplotlib.pyplot as plt
import glob
import csv


y_mins = []
file_list = glob.glob('*.csv')
print('Reading %d files...\n' % len(file_list))

hirokai

Cookbook for image processing in Julia

Image loading, showing, saving

using Images

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

# 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

# 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

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

-- 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

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

# 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)