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View pruning.bsh
// @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
import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
import sc.fiji.analyzeSkeleton.Edge;
import sc.fiji.analyzeSkeleton.Point;
import ij.IJ;
miura / IJ macro course codes
Last active May 9, 2019
IJ macro course codes
View IJ macro course codes
a = 1;
b = 2;
c = a + b;
print( c );
print(a, "+", b, "=", c);
//variables, exercise, an example answer
a = 1;
miura / settings.local.php
Last active May 10, 2018
template settings local file for bise.
View settings.local.php
/** database settings
//$databases['default']['default'] = [
// 'database' => getenv('MYSQL_DATABASE'),
// 'driver' => 'mysql',
// 'host' => getenv('MYSQL_HOSTNAME'),
// 'namespace' => 'Drupal\\Core\\Database\\Driver\\mysql',
View prism_ijm.js
/* */
var _self="undefined"!=typeof window?window:"undefined"!=typeof WorkerGlobalScope&&self instanceof WorkerGlobalScope?self:{},Prism=function(){var e=/\blang(?:uage)?-(\w+)\b/i,t=0,n=_self.Prism={manual:_self.Prism&&_self.Prism.manual,util:{encode:function(e){return e instanceof a?new a(e.type,n.util.encode(e.content),e.alias):"Array"===n.util.type(e)?,"&amp;").replace(/</g,"&lt;").replace(/\u00a0/g," ")},type:function(e){return\[object (\w+)\]/)[1]},objId:function(e){return e.__id||Object.defineProperty(e,"__id",{value:++t}),e.__id},clone:function(e){var t=n.util.type(e);switch(t){case"Object":var a={};for(var r in e)e.hasOwnProperty(r)&&(a[r]=n.util.clone(e[r]));return a;case"Array":return{return n.util.clone(e)})}return e}},languages:{extend:function(e,t){var a=n.util.clone(n.langua
miura /
Created Jul 28, 2017 — forked from tagplus5/
google apps script image to text ocr
function doGet(request) {
if (request.parameters.url != undefined && request.parameters.url != "") {
var imageBlob = UrlFetchApp.fetch(request.parameters.url).getBlob();
var resource = {
title: imageBlob.getName(),
mimeType: imageBlob.getContentType()
var options = {
ocr: true
miura / FRET MAP
Last active Dec 9, 2016 — forked from PMLLancao/FRET MAP
Calculation for FRET Maps.
macro "Ratiometric FRET" {
path = getDirectory("Choose a Directory");
list = getFileList(path);
length = list.length;
File.makeDirectory(path + "Imaging/");
//FRET map creation
miura / gist:6e0682c73e732426c699a5842c0101ce
Created Jul 14, 2016
`fiji --headless` error
View gist:6e0682c73e732426c699a5842c0101ce
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
error importing site
Traceback (most recent call last):
File "/Users/miura/.m2/repository/org/scijava/jython-shaded/2.5.3/jython-shaded-2.5.3.jar/site$py.class", line 62, in <module>
File "/Users/miura/.m2/repository/org/scijava/jython-shaded/2.5.3/jython-shaded-2.5.3.jar/os$py.class", line 50, in <module>
java.lang.ArrayIndexOutOfBoundsException: 8
at org.python.objectweb.asm.ClassReader.a(Unknown Source)
at org.python.objectweb.asm.ClassReader.accept(Unknown Source)
at org.python.objectweb.asm.ClassReader.accept(Unknown Source)
View radialprofile-ext.ijm
run("Blobs (25K)");
run("Radial Profile Angle",
"x_center=127.50 y_center=127.50 radius=127.50 starting_angle=0 integration_angle=180");
run("Clear Results");
for(j = 0; j < Ext.getBinSize; j++){
setResult("Radius", j, Ext.getXValue(j));
setResult("Intensity", j, Ext.getYValue(0, j));
saveAs("results", "");
# subtract mean
from ij import IJ
from ij.process import ImageStatistics as IS
#import math
imp = IJ.getImage()
stack = imp.getStack()
#stat = IS()
for i in range(stack.getSize()):
ip = stack.getProcessor(i + 1)
View gist:84c403b9b9da0a1a94fb
from com.sun.j3d.utils.universe import SimpleUniverse
from com.sun.j3d.utils.geometry import ColorCube
from import BranchGroup
universe = SimpleUniverse()
group = BranchGroup()
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