Image analysis

We developed a number of plug-ins for ImageJ to accomplish common tasks in fluorescence microscopy. ImageJ is a versatile, open source, and extendible image processing program. Much of this software is the result a collaboration with Andre Zeug, Fabian Theis, and Erwin Neher. The plug-ins and examples are available here.

cropped

Blind decomposition of spectrally resolved data – single excitation

Plug-in and documentation available here: PoissonNMF
Example and tutorial
Reference: Blind source separation techniques for the decomposition of multiply labeled fluorescence images. RA Neher, M Mitkovski, F Kirchhoff, E Neher, FJ Theis, A Zeug
Biophysical journal 96 (9), 3791-3800

Blind decomposition of spectrally resolved data – multiple excitation

Plug-in and documentation available here: PoissonNTF
Example and tutorial
Reference: Blind source separation techniques for the decomposition of multiply labeled fluorescence images. RA Neher, M Mitkovski, F Kirchhoff, E Neher, FJ Theis, A Zeug
Biophysical journal 96 (9), 3791-3800

Optimize your choice of excitation wavelength and spectra channel

Plug-in and documentation available here: Optimize Channels
Reference: Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. R Neher, E Neher
Journal of microscopy 213 (1), 46-62

Library of spectra

All our plug-ins use a library of spectra. To get started, a sample library can be download here. Unzip the file and move the folder into the ImageJ plugins folder.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s