volker-baecker’s gists

volker-baecker / exercises.ipynb

Last active July 12, 2021 16:29

Exercises.ipynb

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volker-baecker / run_separate_nuclei.sh

Last active November 21, 2017 13:44

Wrapper script to run the separate_nuclei.ijm macro headless.

	# Run the macro in fiji headlessly using Xvfb
	# to avoid errors due to gui dependencies.
	export DISPLAY=:1
	Xvfb $DISPLAY -auth /dev/null &
	(
	# the ’(’ starts a new sub shell. In this sub shell we start the worker processes:
	java -Xmx6000m -cp jars/ij-1.51l-SNAPSHOT.jar ij.ImageJ -headless --console \
	-macro separate_nuclei.ijm \
	"input=$1, output=$2, scale_factor=$3"
	wait # waits until all ’program’ processes are finished

volker-baecker / separate_nuclei.ijm

Last active November 17, 2017 16:27

Use image scaling and binary watershed to separate the nuclei in the image and create an indexed mask.

	/**
	* Separate Nuclei
	*
	* Use image scaling and binary watershed to separate the nuclei in the image
	*
	* written 2013 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
	*
	* This has been created from
	* http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Separate_Nuclei_Tool
	*

volker-baecker / pong.ijm

Created October 18, 2017 09:54

	/*
	* Play pong on the FIJI example images.
	*
	*/

	var _WIDTH = 800;
	var _HEIGHT = 600;
	var _X_PADDLE = 50;
	var _Y_PADDLE = _HEIGHT / 2;
	var _WIDTH_PADDLE = 10;

volker-baecker / add_ijsegmentclusterednuclei.py

Created April 28, 2017 10:35

add the IJSegmentClusteredNuclei command to cytomine

	import cytomine
	import sys

	#Connect to cytomine, edit connection values

	cytomine_host="my-host" # Cytomine core URL
	cytomine_public_key="my-public-key" # Your public key
	cytomine_private_key="my-private-key" # Your private key
	id_project=my-project-id

volker-baecker / IJSegmentNuclei.py

Last active January 28, 2018 12:07

wrapper script to run the IJSegmentNuclei workflow from cytomine

	import sys
	import os
	from cytomine import Cytomine
	from cytomine.models import *
	from subprocess import call
	from skimage import io
	import numpy as np
	from sldc import locator
	from sldc.locator import affine_transform
	from shapely.ops import cascaded_union

volker-baecker / run-segment-clustered-nuclei.sh

Last active April 25, 2017 13:22

run the IJSegmentClusteredNuclei.ijm macro in xvfb

	# Run the metrics-macro in ImageJ headlessly using Xvfb to avoid errors due to ImageJ1 gui dependencies.

	export DISPLAY=:1
	Xvfb $DISPLAY -auth /dev/null &
	(
	# the '(' starts a new sub shell. In this sub shell we start the worker processes:

	java -Xmx6000m -cp jars/ij-1.51l-SNAPSHOT.jar ij.ImageJ -headless --console -macro IJSegmentClusteredNuclei.ijm "input=$1, output=$2, radius=$3, threshold=$4"
	wait # waits until all 'program' processes are finished
	# this wait sees only the 'program' processes, not the Xvfb process

volker-baecker / IJSegmentClusteredNuclei.ijm

Last active April 28, 2017 10:20

Segment clustered nuclei with FIJI

	// Author: Sébastien Tosi (IRB Barcelona)
	// modified by Volker Bäcker to make it run
	// in batch mode, reading parameters from the command line
	//
	// The macro will segment nuclei and separate clustered nuclei
	// using a binary watershed. As a result an index-mask image is
	// written for each input image.
	// Use FIJI to run the macro with a command similar to
	// java -Xmx6000m -cp jars/ij.jar ij.ImageJ -headless --console -macro IJSegmentClusteredNuclei.ijm "input=/media/baecker/donnees/mri/projects/2017/liege/in, output=/media/baecker/donnees/mri/projects/2017/liege/out, radius=5, threshold=-0.5"

volker-baecker / WG5-TG3_batch_extract_middle_slices.ijm

Last active September 27, 2017 08:44

A simple macro to extract the middle slices of a number of input stacks.

	// For all images in a folder, extract the middle slice and save it into a
	// subfolder.
	//
	// Written 2017 by Volker Baecker, Montpellier Ressources Imagerie


	var _FILE_EXTENSION = ".tif";

	setBatchMode(true);
	dir = getDirectory("Select the input folder!");

volker-baecker / run-metrics.sh

Last active February 1, 2017 14:38

	# Run the metrics-macro in ImageJ headlessly using Xvfb to avoid errors due to ImageJ1 gui dependencies.

	export DISPLAY=:1
	Xvfb $DISPLAY -auth /dev/null &
	(
	# the '(' starts a new sub shell. In this sub shell we start the worker processes:

	java -Xmx6000m -cp jars/ij-1.51h.jar ij.ImageJ -headless --console -macro metrics.ijm "plugin=$1, dir=$2, table=/fiji/data/in/Results.xls"
	wait # waits until all 'program' processes are finished
	# this wait sees only the 'program' processes, not the Xvfb process

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