kwolbachia’s gists

kwolbachia / RGBroll.ijm

Created April 26, 2022 18:04

imagej macro to create an animation with Hue rotation on a rgb image

	//heavily inspired by Jerome Mutterer at https://gist.github.com/mutterer/883b32fb4dd7d9bcbd9a1ee32f1a2fd9
	//Thanks!
	macro "RGBroll"{
	hues=30;
	setBatchMode(1);
	run("Duplicate...","title=temp");
	run("Size...", "width="+Image.width+" height="+Image.height+" depth="+hues+" constrain average interpolation=Bilinear");
	run("HSB Stack");
	Stack.getDimensions(width, height, channels, slices, frames);
	Stack.setChannel(1);

kwolbachia / inverted_overlay.ijm

Created December 15, 2021 12:43

imagej macro script to invert an image and keep the original colors

	// Kevin Terretaz @kWolbachia
	// highly inspired by Jerome Mutterer script : https://forum.image.sc/t/invert-rgb-image-without-changing-colors/33571/8
	macro "inverted overlay" {
	setBatchMode(1);
	title = getTitle();
	rgbSnapshot();
	run("Invert");
	run("HSB Stack");
	run("Macro...", "code=v=(v+128)%256 slice");
	run("RGB Color");

kwolbachia / frozenLake.lut

Created December 5, 2021 16:59

imageJ LUT based on https://twitter.com/guijacquemet/status/1467488616901488640?s=20

kwolbachia / new_LUT_from_selection.ijm

Last active November 10, 2021 17:04

generates a full LUT from part of an existing one. Offrande au grand manitou des LUTs!

	// Kevin Terretaz @kwolbachia 10.11.21
	// open the LUT you want to transform as a 256x32 8bit image
	// run the macro
	run("Select All");
	waitForUser("adjust the selection to crop");
	setBatchMode(1);
	run("Duplicate...","duplicate");
	run("RGB Color");
	run("Scale...",
	"x=- y=- width=256 height=65 interpolation=Bicubic average create");

kwolbachia / gamma_LUT.groovy

Created November 9, 2021 17:04

gamma adjustment on LUTs with cursor

	//Kevin Terretaz 061021
	import ij.*
	import ij.gui.*
	import ij.process.*
	import java.awt.image.*

	// gammaLUT avec curseur
	//possible pour les hyperstacks d'ajuster autant de curseurs que de channels en même temps?
	imp = IJ.getImage()
	luts = new LUT[0]

kwolbachia / multichannel_profile_plot.ijm

Last active September 24, 2021 09:28 — forked from mutterer/multichannel_profile_plot.ijm

	// yet another multichannel profile plotter
	// with smart lookuptables
	// modified and simplified to my tastes + "better" LUT detection

	macro "Multiplot" {
	id=getImageID();
	getDimensions(width, height, channels, slices, frames);
	if (selectionType()==-1) exit;
	Stack.getPosition(Channel, slice, frame);
	getPixelSize(unit, pixelWidth, pixelHeight);

kwolbachia / Splitview.ijm

Last active April 15, 2021 18:26

imageJ Fiji Splitview macro

	/*----------------------------------------------------------------------------------------------------------------------
	For multichannel visualization, 5 channel max
	This macro will generate a montage of composite and splited channels in one RGB Image
	You can still navigate through slices or frames.
	Note : the Splitview image size can be heavy on big hyperstacks due to RGB conversion
	Advice : draw a selection before running Spliview, the produced montage will be croped
	The new version can ask tu user channel labels and add it in the Splitview with color corresponding to each LUTs.
	----------------------------------------------------------------------------------------------------------------------*/
	var ChLabels = newArray("GFP","RFP","fRFP","DAPI","Brightfield");
	var fontS = 30;

kwolbachia / gammaLUT.ijm

Last active April 15, 2021 18:27

imageJ Fiji Gamma LUTs macro

	/*
	15/04/21 K Terretaz @kWolbachia
	visual gamma correction applied on active LUT or all channel LUTs, no modification of pixels data
	VERY much inspired by https://github.com/ndefrancesco/macro-frenzy/blob/master/color/gammify_LUT.ijm for its simplicity
	and https://imagej.nih.gov/ij/macros/Gamma_LUT.txt for non linear LUTs compatibility
	*/

	macro "gammaLUT on all channels" {
	setGammaLUTAllch(getNumber("gamma",0.7));
	}

Kevin Terretaz kwolbachia