Kota Miura miura
miura
/ FRET MAP
Last active
December 9, 2016 21:30
— forked from PMLLancao/FRET MAP
Calculation for FRET Maps.
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| 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
July 14, 2016 11:59
`fiji --headless test.py` error
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| 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) |
miura
/ radialprofile-ext.ijm
Created
July 13, 2016 11:55
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| 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", ""); |
miura
/ subtractMean.py
Created
July 21, 2015 15:25
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| # 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) |
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| 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) |
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| cc=0; | |
| for(k=0; k<nSlices; k++) | |
| for(j=0;j<getHeight();j++) | |
| for(i=0;i<getWidth();i++) | |
| {setSlice(k+1);if(getPixel(i,j)>0)cc++;} | |
| print("non-0:" + cc); |
miura
/ gist:7de5c97c761ea867c8cb
Last active
August 29, 2015 14:11
— forked from mhawksey/gist:1170597
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| function onOpen() { | |
| var menuEntries = [ {name: "Create Diary Doc from Sheet", functionName: "createDocFromSheet"}]; | |
| var ss = SpreadsheetApp.getActiveSpreadsheet(); | |
| ss.addMenu("Fitness Diaries", menuEntries); | |
| } | |
| function createDocFromSheet(){ | |
| var templateid = "1O4afl8SZmMxMFpAiN16VZIddJDaFdeRBbFyBtJvepwM"; // get template file id | |
| var FOLDER_NAME = "Fitness Diaries"; // folder name of where to put completed diaries | |
| // get the data from an individual user |
miura
/ gist:d19f8f51bb489d66d2ff
Created
December 8, 2014 15:59
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| // *** Start: White balance *** | |
| name=getTitle(); | |
| run("Split Channels"); | |
| MeanColor=newArray(3); | |
| maxi = 0; | |
| for (u=1; u<4; u++) { | |
| selectWindow("C"+u+"-"+name); | |
| makeRectangle(100,100,100,100); | |
| // waitForUser("Please draw a region in the background"); |
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| scale = 0.083; // マイクロメータ/ピクセル | |
| dt = 3; // 秒/フレーム | |
| path = File.openDialog("Select a File"); | |
| str = File.openAsString(path); | |
| strA = split(str, "\n"); | |
| // データ格納用の配列の用意 | |
| dispA = newArray(strA.length - 13); | |
| intdispA = newArray(strA.length - 13); |
miura
/ gist:e6d67384640129b5b89f
Created
September 16, 2014 09:13
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| ''' | |
| Tiff file resolution checker | |
| ''' | |
| from ij.io import TiffDecoder | |
| from ij.io import DirectoryChooser | |
| from ij import IJ | |
| import os | |
| def xresGetter(d, filename): |