imagejan

#@ File (style="extension:bmf") meshFile
#@ File (style="save") newMeshFile
#@ ImagePlus intensity_image
#@ LogService log
#@ Double (value=200.0) gamma
#@ Double (value=3.0) alpha
#@ Double (value=0.0) pressure
#@ Double (value=0.0) steric_neighbors
#@ Double (value=0.0002) image_weight
#@ Integer (value=2) divisions

imagejan

#@ Dataset input
#@ OpService ops
#@ Integer (label="Width of sliding window (frames)") window
#@output projected

// Add a new dimension of window size
added = ops.transform().addDimensionView(input, 0, window-1)
extended = ops.transform().extendBorderView(added)

// Shear along time dimension,

imagejan

/**
 * This ImageJ script opens the icon from a given file
 * (as displayed in the operating system) as an ij.ImagePlus
 */

#@ File iconFile

import sun.awt.shell.ShellFolder
import ij.ImagePlus
import ij.process.ColorProcessor

imagejan

#@ Dataset input
#@ OpService ops
#@ DatasetService ds
#@ ConvertService cs

import net.imagej.axis.Axes
import net.imglib2.IterableInterval
import net.imglib2.type.numeric.integer.UnsignedShortType
import ij.CompositeImage
import ij.ImagePlus

imagejan

Verifying my Blockstack ID is secured with the address 1LyvZSDS5vYQdFXivZDsamwieqbieaFRAT https://explorer.blockstack.org/address/1LyvZSDS5vYQdFXivZDsamwieqbieaFRAT

imagejan

# see http://blog.neutrino.es/2012/git-copy-a-file-or-directory-from-another-repository-preserving-history/

mkdir /tmp/mergepatchs
cd ~/repo/org
export reposrc="path/to/file1 path/to/file2"
git format-patch -o /tmp/mergepatchs $(git log $reposrc|grep ^commit|tail -1|awk '{print $2}')^..HEAD $reposrc
cd ~/repo/dest
git am /tmp/mergepatchs/*.patch

imagejan

/*
 * Open an XML file saved by Cell Counter as an ImageJ PointRoi (ignoring stack position)
 *
 * (see https://forum.image.sc/t/convert-cell-counter-markers-to-multi-point/23844?u=imagejan)
 */

#@ ImagePlus imp
#@ File input

import groovy.xml.XmlParser

imagejan

#@ Img input
#@ OpService ops

import net.imglib2.algorithm.stats.Max

histogram = ops.run("histogram", input)
cursor = Max.findMax(histogram)
value = input.firstElement().copy()
histogram.getCenterValue(cursor.getLongPosition(0), value)

imagejan

import ij.WindowManager

/**
 * Get all open images as list of {@code ImagePlus}
 */
def getImagesAsList() {
	count = WindowManager.getImageCount()
	return (1..count).collect { WindowManager.getImage(it) }
}

imagejan

#@ ImagePlus imp
#@ File (style = "directory", label = "Output folder") outputFolder
#@ String (label = "Output file name") filename
#@ double (label = "Spot radius", stepSize=0.1) radius
#@ double (label = "Quality threshold") threshold
#@ int (label = "Max frame gap") frameGap
#@ double (label = "Linking max distance") linkingMax
#@ double (label = "Gap-closing max distance") closingMax

import fiji.plugin.trackmate.Model