Skip to content

Instantly share code, notes, and snippets.

Kota Miura miura

Block or report user

Report or block miura

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
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
// 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
miura / IJ macro course codes
Last active May 9, 2019
IJ macro course codes
View IJ macro course codes
//variables
a = 1;
b = 2;
c = a + b;
print("\\Clear");
print( c );
print(a, "+", b, "=", c);
//variables, exercise, an example answer
a = 1;
@miura
miura / settings.local.php
Last active May 10, 2018
template settings local file for bise.
View settings.local.php
<?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
/* http://prismjs.com/download.html?themes=prism&languages=markup+css+clike+javascript+markdown&plugins=line-numbers+file-highlight */
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)?e.map(n.util.encode):e.replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/\u00a0/g," ")},type:function(e){return Object.prototype.toString.call(e).match(/\[object (\w+)\]/)[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 e.map(function(e){return n.util.clone(e)})}return e}},languages:{extend:function(e,t){var a=n.util.clone(n.langua
@miura
miura / imageToText.gs
Created Jul 28, 2017 — forked from tagplus5/imageToText.gs
google apps script image to text ocr
View imageToText.gs
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
miura / FRET MAP
Last active Dec 9, 2016 — forked from PMLLancao/FRET MAP
Calculation for FRET Maps.
View FRET MAP
macro "Ratiometric FRET" {
path = getDirectory("Choose a Directory");
list = getFileList(path);
length = list.length;
File.makeDirectory(path + "Imaging/");
//FRET map creation
@miura
miura / gist:6e0682c73e732426c699a5842c0101ce
Created Jul 14, 2016
`fiji --headless test.py` 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));
}
updateResults();
saveAs("results", "");
View subtractMean.py
# 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 javax.media.j3d import BranchGroup
universe = SimpleUniverse()
group = BranchGroup()
group.addChild(ColorCube(0.3))
universe.getViewingPlatform().setNominalViewingTransform()
universe.addBranchGraph(group)
You can’t perform that action at this time.