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Techn. Fakultät Willkommen am Institut für Informatik FAU-Logo

Dipl.-Inf. Markus Mayer

Alumnus of the Pattern Recognition Lab of the Friedrich-Alexander-Universität Erlangen-Nürnberg

The vision of my work is to develop image processing methods that provide new tools for ophthalmologists to ease the detection of glaucoma and related eye diseases.

Programs & Code

On this site programs and code that I have worked on during my research are published. Use them as you want but at your own risk. If you find something useful, I would be grateful if you would look around this website for articles that you find worth citing in your next publication. May them be from myself or my colleagues.

OCTSEG

OCTSEG (Optical Coherence Tomography Segmentation and Evaluation GUI) is a graphical user interface written by me in MATLAB for research purpose. The software is used in clinical studies in my collaboration with the ophthalmic department of the university clinic Erlangen.

 

The retinal layers and the blood vessels of retinal OCT scans can be segmented. In addition, tools for the manual correction of the automated segmentations and the visualization of the data are provided.

 

You'll find additional information and a download here: OCTSEG

Matlab Code: Denoising Algorithms

I implemented commonly used and state-of-the-art denoising algorithms in the Image Denoising Algorithms Archive (IDAA), including various diffusion algorithms (Anisotropic Diffusion, Complex Diffusion), wavelet thresholding, Bayesian estimation denoising...

 

The IDAA website was originally created out of the Projekt OCT Image Denoising, and we plan to compare several of the algorithms shown here for the purpose of denoising OCT images in an upcoming publication. However, the archive is intended to be useful for multiple purposes and various modalities.

 

I currently use the denoising codes in my project Automated Retinal Layer Segmentation and in my OCTSEG programm for denoising OCT images with complex diffusion.

Matlab Code: Opening Heidelberg Engineering Spectralis .vol Raw Data Files

The OCT scans of the Heidelberg Engineering Spectralis OCT may be exported in a RAW data format. The filenames of these data files usually end with ".vol". For image processing research, it is of interest to work directly with the 32bit floating point data stored in the RAW files. Radim Kolar (Brno University, Czech Republic) wrote a Matlab function to access the data, modified by me (Markus Mayer, Pattern Recognition Lab, University of Erlangen-Nuremberg, Germany). An additional bugfix was added by Kris Sheets (Retinal Cell Biology Lab, Neuroscience Center of Excellence, LSU Health Sciences Center, New Orleans, USA).

 

You can download the code here: openVol.m

 

I use this code in all my OCT related projects, i.e. Automated Retinal Layer Segmentation, OCT Image Denoising and in my OCTSEG programm.

 

If you are searching for other ways to access the .vol-Files, you might want to have a look at the "Open Heyex Raw Files" ImageJ Plugin written by Kris Sheets (Retinal Cell Biology Lab, Neuroscience Center of Excellence, LSU Health Sciences Center, New Orleans, USA).