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import os
import re

import tifffile

# adjust to dataset:
input_dir = "PATH_TO_TIFFS"
pixel_size = 0.225
maximum_shift_microns = 50

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'use strict';
const fs = require('fs');
var http = require('http');
http.createServer(function (req, res) {
    res.setHeader("Content-Type", "text/html");
    let rawdata = fs.readFileSync('imagej-imagej.json');
    let room = JSON.parse(rawdata);
    room.sort(function(a,b) {
      if ( a.sent < b.sent )
          return -1;

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#@ File (label = "Input directory", style = "directory") input
#@ File (label = "Output directory", style = "directory") output
#@ String (label = "File suffix", value = ".jpg") suffix

processFolder(input);

function processFolder(input) {
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) {

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https://imagej.net/Scripting_Headless

Start a SciJava command from command line:
./ImageJ-linux64 --run org.scijava.plugins.commands.debug.DumpStack

.. headless:
./ImageJ-linux64 --headless --run org.scijava.plugins.commands.debug.DumpStack

Calling a script from command line:
./ImageJ-linux64 --ij2 --headless --console --run hello.py 'name1="Mr",name2="Mrs Kraken"'

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// creating images
Object img1 = ij.io().open("https://samples.fiji.sc/blobs.png");
Object img2 = ij.io().open("https://samples.fiji.sc/new-lenna.jpg");

// showing images
ij.ui().show(img1);
ij.ui().show(img2);

// get images
List<Dataset> datasets = ij.dataset().getDatasets();

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Installing Nightscout on DigitalOcean Server

Why?

• You have full SSH access to your server
• Creating a server takes a minute
• You can choose from various places on earth where the server should be located
• You can make a backup / snapshot of the server in order to delete and later restore it (saves money if you don't need it for a while)
• You pay per hour, the $5 / month version should be sufficient
• Loads of documentation on how to install things
• Control and track the server via the DigitalOcean control panel website

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Where to find and add algorithms in ImageJ

If you are as confused as I am about how to distinguish algorithms, scripts, macros, plugins, ops, commands and modules, welcome to this page.

TODO needs a class hierarchy view

Space of action

ImgLib2 algorithms

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src

../../../addons/ofx2DMapping/src
../../../addons/ofxAccelerometer/src
../../../addons/ofxBlur/src
../../../addons/ofxBox2d/src
../../../addons/ofxBox2d/src/lib/Box2D/Include
../../../addons/ofxBox2d/src/lib/Box2D/Source/Collision
../../../addons/ofxBox2d/src/lib/Box2D/Source/Collision/Shapes
../../../addons/ofxBox2d/src/lib/Box2D/Source/Common