SpotDistance

An ImageJ plugin for evaluate intra-nuclear 3D cross-distances between fluorescent spots in multi-channel images

Written by Daniel Sage at the Biomedical Image Group, EPFL, Switzerland

splash image

Outline

This ImageJ's plugin determines intra-nuclear 3D cross-distances between fluorescent spots in multi-channel z-stack of images.

Reference

H. Schober, V. Kalck, M.A. Vega-Palas, G. Van Houwe, D. Sage, M. Unser, M.R. Gartenberg, S.M. Gasser, "Controlled Exchange of Chromosomal Arms Reveals Principles Driving Telomere Interactions in Yeast," Genome Research, vol. 18, no. 2, pp. 261-271, February 2008.

Software

Specification

This ImageJ's plugin determines intra-nuclear 3D cross-distances between fluorescent spots in multi-channel z-stack of images. The plugins first locates the nucluei on a average-intensity projection, hence it assumes to have on layer on cells. In the second step, it determines the postion of the fluorescent spot on a filtered version of the image. The filter used is a 3D Laplacian of Gaussian (Mexican Hat) which enhances the small brigth spots. The plugin reports the cross-distance in a table which can be export in a spreadsheet (Excel).
This plugin has been developped to evaluate the telomere to telomere distance inside a nucleus in the budding yeast.

Pre-requirement

The software provided here is a plugin for ImageJ, a general purpose image-processing and image-analysis package. It runs also on the image-processing package Fiji. ImageJ has a public domain licence; it runs on several plateforms: Unix, Linux, Windows, and Mac OS X. It doesn't take more than a couple of minutes to install.

Download

Download SpotDistance_.jar, the ImageJ's plugin. The plugin consists in one single JAR file; place it into the "plugins" folder of ImageJ. Do not unzip the JAR file.

Instructions

Start ImageJ and launch the plugin SpotDistance.
Select the number of channels to be processed.
Open Images: the plugin opens three z-stack of images of the same size. The convention for the filename is the following «root»«suffix».«extension». The suffix have to be set in the dialog box by the user. The root is determines automatically when the user choose the first stack of images.
The plugin automatically build a color stack of images and a 2D image which is a average intensity projection to display the results.
Select the right parameters of the processing. To choose the parameters, it exist a button "Test" which process only one channel and show the intermediate results.
Click on "Measure" to start the whole process. Be patient !
The table show all the cross-distances and the position, by choosing "Copy" the user can export the results.
The "Screenshot" button produces a RGB image.

Conditions of use

You are free to use this software for research purposes, but you should not redistribute it without our consent.
In addition, we expect you to include adequate citations and acknowledgments whenever you present or publish results that are based on it.

Test images

A small z-stacks of images are available for testing. To get it, download sample-spotdistance.zip [1.8 Mb] and unzip the file. It contains 3 stacks of 16 images of 256x200 pixels.

Screenshot

Acknowledgements

Heiko Schober and Susan Gasser, Freidrich Meischer Institute for Biomedical Research, Basel, Switzerland.
Krestin Bystricky, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse, France

daniel.sage@epfl.ch • 20.08.2014