Retina Imaging Toolbox (RIT)

Content

• Introduction
• Image registration
• Vessel segmentation
• Blind source separation
• K-means filter for spike noise suppression
• Time-course morphology analysis via control points
• Automated pipelines
• References

Introduction

ANYONE CAN CONTRIBUTE to the open-source MATLAB/Octave software library for automated dynamic or static retina image analysis. The library includes:

• import of standard video file formats (e.g. .avi, .mp4, .mkv, etc.) into 3D double array variable
• rigid image registration (Kolar et al. 2016)
• blind source separation (i.e. principal component analysis - PCA, independent component analysis - ICA) (Labounkova et al. 2019; Labounkova et al. 2021; Hyvarinen and Oja 1997)
• one-dimensional spike noise suppresion K-means filter (Labounkova et al. 2021)
• automatic detection of control points in periodic time-courses (Labounkova et al. 2021)
• visualization of spatial color-coded statistical parametric map over a retina anatomy background image

In the near future, we plan to rewrite RIT into a paralell and separate full python implementation and build graphical interface for comfortable and easy result visualization.

Image registration

[In Progress]

Vessel segmentation

[In Progress]

Blind source separation

[In Progress]

K-means filter for spike noise suppression

[In Progress]

Time-course morphology analysis via control points

[In Progress]

Automated pipelines

[In Progress]

References

Hyvarinen, A., Oja, E. (1997). A Fast Fixed-Point Algorithm for Independent Component Analysis. Neural Computation, 9, 1483-1492. DOI: 10.1162/neco.1997.9.7.1483

Kolar, R., Tornow, R. P., Odstrcilik, J., & Liberdova, I. (2016). Registration of retinal sequences from new video-ophthalmoscopic camera. Biomedical Engineering Online, 15(1), 57. DOI: 10.1186/s12938-016-0191-0

Labounkova, I., Labounek, R., Nestrasil, I., Odstrcilik, J., Tornow, R.P., & Kolar, R. (2021). Blind Source Separation of Retinal Pulsatile Patterns in Optic Nerve Head Video-Recordings. IEEE Transactions on Medical Imaging, 40(3), 852-864 DOI: 10.1109/TMI.2020.3039917

Labounkova, I., Labounek, R., Odstrcilik, J., Hracho, M., Nestrasil, I., Tornow, R. P., & Kolar, R. (2019). Blind Source Separation of Different Retinal Pulsatile Patterns from Simultaneous Long-term Binocular Ophthalmoscopic Video-records. In 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 4729-4732. DOI: 10.1109/EMBC.2019.8857560