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Curtis Rueden ctrueden

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ctrueden /
Last active Oct 30, 2019
Open images as numpy arrays using SCIFIO and Bio-Formats
#!/usr/bin/env python
# - Open images as numpy arrays using SCIFIO and Bio-Formats.
# -- Settings --
max_mem_mb = '6144'
scifio_lifesci = False
ctrueden /
Created Sep 22, 2019
How to diff the API of two JAR files
# TODO: Why doesn't this work
trap "exit" INT
die() {
echo "$1" 2>&1
exit 1
ctrueden / charting-extension.pom
Last active Sep 20, 2019
Unifying multiple POMs at different BOM versions
View charting-extension.pom
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="" xmlns:xsi="" xsi:schemaLocation="">
<name>Charting Plugin</name>
ctrueden / Vertical_Stacker.groovy
Created Sep 11, 2019
Create a vertical stack of images, each horizontally centered
View Vertical_Stacker.groovy
#@ ImageJ ij
#@ File[] imageFiles
#@ File(style = "save") outFile
#@ boolean showStack
import java.util.Arrays
import net.imglib2.FinalInterval
import net.imglib2.type.numeric.integer.UnsignedByteType
import net.imglib2.util.Intervals
ctrueden / Generative_Image.groovy
Created Jun 18, 2019
Generate an image from a function in ImageJ
View Generative_Image.groovy
#@ Long(value = 3000) size
import java.util.function.BiConsumer
import net.imglib2.img.display.imagej.ImageJFunctions
import net.imglib2.position.FunctionRandomAccessible
import net.imglib2.type.numeric.integer.UnsignedByteType
import net.imglib2.view.Views
// Define a function in 2-space.
ndim = 2
ctrueden /
Last active May 21, 2019
Import a cropped region of a 2D image using SCIFIO
#@ DatasetIOService dio
#@ File imageFile
#@ long x
#@ long y
#@ long width
#@ long height
#@output Dataset dataset
from io.scif.config import SCIFIOConfig
from io.scif.img import ImageRegion, Range
ctrueden / boofcv-seeded-watershed.groovy
Last active Mar 25, 2019
Seeded watershed in ImageJ using BoofCV
View boofcv-seeded-watershed.groovy
#@dependency(group="org.boofcv", module="boofcv-core", version="0.33")
#@dependency(group="org.boofcv", module="boofcv-swing", version="0.32")
#@both ImagePlus imp
#@output ImagePlus (label="Watersheds") watersheds
#@output ImagePlus (label="Regions") regions
#@output ImagePlus (label="Seeds") seeds
import boofcv.alg.filter.binary.BinaryImageOps
import boofcv.alg.filter.binary.ThresholdImageOps
ctrueden / ImageJ1-with-Jython-via-BeakerX.ipynb
Last active Mar 22, 2019
Use Jython to invoke ImageJ 1.x API in a BeakerX Groovy notebook
View ImageJ1-with-Jython-via-BeakerX.ipynb
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ctrueden / Open-as-numpy-array-via-Bio-Formats.ipynb
Last active Apr 20, 2019
Open an image with Bio-Formats as a numpy array via pyimagej
View Open-as-numpy-array-via-Bio-Formats.ipynb
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ctrueden / automatic-module-names.log
Created Mar 1, 2019
Fiji dependencies Automatic-Module-Name entries
View automatic-module-names.log
$ for jar in $(mvn dependency:build-classpath | grep -A1 'Dependencies classpath' | tail -n1 | gsed 's/:/\n/g') # C 1 {2019-03-01 16:41:33}
if [ -f "$jar" ]
autoModule=$(unzip -q -c "$jar" META-INF/MANIFEST.MF | grep 'Automatic-Module')
if [ "$autoModule" ]
echo "$jar: $autoModule"
# else
# echo "$jar: Automatic-Module ENTRY IS MISSING"
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