miura

from ij import ImagePlus, IJ
from emblcmci import BleachCorrection

url = "/home/miura/yeastNucleus2DT.tif"
imp = ImagePlus(url)
print imp.getStackSize()

bc = BleachCorrection()

### simple rtio method

miura

from ij import IJ
from ij3d import Image3DUniverse, Content

flyurl = "http://imagej.nih.gov/ij/images/flybrain.zip"
imp = IJ.openImage(flyurl)
univ = Image3DUniverse()
univ.show()
c = univ.addVoltex(imp)

from ij import ImagePlus, ImageStack

miura

{
    "WFE_output_params_file": "wfe_module_params_1.json",
    "3d_image_stack" : "/input/Skeleton.tif",
    "prune_cycle_method": "shortest branch",
    "prune_ends": false            
}

miura

<?php

/** database settings
**/

//$databases['default']['default'] = [
//  'database' => getenv('MYSQL_DATABASE'),
//  'driver' => 'mysql',
//  'host' => getenv('MYSQL_HOSTNAME'),
//  'namespace' => 'Drupal\\Core\\Database\\Driver\\mysql',

miura

// @ImagePlus(label="Skeleton image", description="Binary image skeletonized with Skeletonize3D") image
// @double(label="Length threshold", description="Minimum branch length to keep") threshold
// @OUTPUT ImagePlus prunedImage

// https://forum.image.sc/t/skeletonize-remove-or-prune-short-end-segments/4704

import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
import sc.fiji.analyzeSkeleton.Edge;
import sc.fiji.analyzeSkeleton.Point;
import ij.IJ;

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

// ImageJ macro

//*** change the window title here, depending on your input image. 
OriginalTitle = "BloodVessels_small.tif";

// following window titles are always same. 
LabelMask = "FastFiltered_Tubeness_LabelMask.tif";
tagged = "FastFiltered_Tubeness_LabelMask_Skeleton_tagged_skeleton.tif";
VisualisationDilation = 2;
Nthreads = 4;

miura

\lstdefinelanguage{IJM}{%
  language     = Java,
  morekeywords = {var, macro, return, function, get, set, is, 
  abs, acos, Array, asin, atan, atan2, autoUpdate, beep, bitDepth, calibrate, call, changeValues, charCodeAt, close, cos, d2s, debug, Dialog, doCommand, doWand, drawLine, drawOval, drawRect, drawString, dump, endsWith, eval, exec, exit, exp, File, fill, fillOval, fillRect, Fit, floodFill, floor, fromCharCode, getArgument, getBoolean, getBoundingRect, getCursorLoc, getDateAndTime, getDimensions, getDirectory, getDir, getDisplayedArea, getFileList, getFontList, getHeight, getHistogram, getImageID, getImageInfo, getInfo, getLine, getList, getLocationAndSize, getLut, getMetadata, getMinAndMax, getNumber, getPixel, getPixelSize, getProfile, getRawStatistics, getResult, getResultString, getResultLabel, getSelectionBounds, getSelectionCoordinates, getSliceNumber, getStatistics, getString, getStringWidth, getThreshold, getTime, getTitle, getValue, getVoxelSize, getVersion, getWidth, getZoom, IJ, imageCalcul

miura

//20200909 Kota Miura
// temporal colorcode fix

testpath = "/Users/miura/Desktop/tmp/rewritemacro/Temporal-Color_Code.ijm";
ijmpath = testpath;

ijpluginDir = getDir("plugins");
thefile = ijpluginDir + "Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm";
ijmpath = thefile;

miura

//variables
a = 1;
b = 2;
c = a + b;
print("\\Clear");
print( c );
print(a, "+", b, "=", c);

//variables, exercise, an example answer
a = 1;