- 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
Deborah Schmidt frauzufall
frauzufall
/ benchmark_dask_slicing.ipynb
Created
July 26, 2025 04:11
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frauzufall
/ benchmark_bioio_vs_native.py
Last active
July 5, 2025 17:56
Benchmarking bioio vs native readers
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| # /// script | |
| # dependencies = [ | |
| # "numpy", | |
| # "pillow", | |
| # "tifffile", | |
| # "imageio", | |
| # "bioio", | |
| # "bioio-tifffile", | |
| # "bioio-imageio", | |
| # "matplotlib", |
frauzufall
/ align_tiffs_with_ashlar.py
Last active
September 21, 2023 18:54
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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; |
frauzufall
/ gist:bcac3921d2ea6e0f19cd5edfba0df794
Created
August 9, 2019 11:37
Macro running skeleton analysis in batch mode
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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++) { |
frauzufall
/ ImageJ command line execution
Last active
June 11, 2022 11:10
ImageJ command line execution
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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"' |
frauzufall
/ Get all open images in ImageJ.java
Last active
June 26, 2019 20:15
Get all open images in ImageJ
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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(); |
frauzufall
/ Nightscout on DigitalOcean Server.md
Last active
March 21, 2021 02:34
frauzufall
/ Where to find and add algorithms in ImageJ.md
Last active
September 26, 2017 23:12
frauzufall
/ of_example.includes
Created
February 26, 2016 09:35
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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 |