Software

One of the main focus areas of the AOIP is the development of advanced image processing and visualization software that enables integration of imaging data from the most advanced OCT instruments with that obtained from our adaptive optics imaging systems.  The result is the most detailed, comprehensive look at retinal disease in the living eye that we have ever had.  We are happy to share many of our software tools, please contact us via email if you are interested in any of the software described below.

DeMotion

The human eye is constantly in motion, even when we try our best to focus on steady object.  When trying to image the living retina, these eye movements can make it difficult to obtain high quality images.  Some patients have nystagmus (rapid, large amplitude eye movements), which results in even more severe instability. DeMotion (written by Dr. Alfredo Dubra and Zach Harvey) is a software that can align and average the images from the Adaptive Optics Scanning Light Ophthalmoscope (AOSLO) to improve image quality and allow us to visualize the smallest structures in the retina.  Shown below is an example of how DeMotion works.

normal unstabilized movie of a normal human cone mosaic
A raw AOSLO movie of a normal human cone mosaic - note the high degree of motion.
demotion stabilization
The same movie stabilized with DeMotion software and with low quality frames removed.
Demotion, aligned and averaged image
The final aligned, averaged image.  These images are then used for subsequent analysis.

 

Cone Counting

cone counting softwareOne of the more basic analyses we can perform on images of the photoreceptor mosaic is to count the cells of interest to determine their density.  Also of interest is the overall packing geometry of the photoreceptor mosaic, with the idea that such quantitative metrics may provide sensitive biomarkers with which to track disease progression and monitor treatment response in various retinal conditions. To address this, we built upon the cell counting method by Li and Roorda, to implement both a fully-automated and semi-automated version, and we recently characterized the repeatability of this method in a paper by Garrioch et al.

Shown on the left is what the user interface of the software looks like. After the program has automatically identified about 90% of the cones, the user has the option of adding cones missed by the algorithm, subtracting cones identified in error, or adjusting the position of the cone marker.

 

Shown below is an example of a single image of the parafoveal cone mosaic along with the corresponding cone locations marked by the algorithm.  These cone locations can be read into various other programs to compute the density of the cones, their average spacing, and/or the packing geometry of this particular patch of retina.

Parafoveal cone mosaic
Image of the normal parafoveal cone mosaic.
Parafoveal cone mosaic - cone locations marked
Same image, cone locations marked in green.

 

OCT Volume Visualizer – (OCT-VV)

OCT provides unparalleled axial resolution, and conventional analysis of OCT images focuses on the appearance of the various layers of the retina.  While this is informative, it makes it difficult to appreciate how structures in one OCT image are related or connected to structures in another OCT image.  Given the ability to acquire dense volumetric OCT scans (in which many B-scans are taken over a large retinal area), there are new visualization techniques emerging. Many investigators are now using an "en face" visualization approach, in which the pixels in the OCT B-scans are summed together to create a single gray-level pixel value at each location within the OCT volume.  This is sometimes referred to as a summed volume projection (SVP), volume intensity projection (VIP) or a C-scan.  More detailed en face images can be generated by using only certain portions of the OCT image, though this is complicated by the changing contour of the retina throughout an OCT volume and the large number of B-scans often acquired.  The AOIP OCT Volume Visualizer (OCT-VV) enables creation of a custom contour for each B-scan within a volume, and is designed to work with OCT volumes from any of the major OCT systems.


En face images generated from OCT volumes from two patients with advanced choroideremia.  These images were created using the OCT-VV software, however the contour was confined to the outer retinal layers (outer nuclear layer and photoreceptor layers).  The individual B scans reveal circular structures in these layers, which have been referred to as outer retinal tubulation.  The inter-connectedness of the tubules can easily be seen in the SVP images, and these images can then be co-registered with other more conventional retinal images (such as fundus autofluorescence).  See the ARVO poster by Rha et al for more findings on choroideremia.

 

Advanced Ocular Imaging Program
Eye Institute
925 North 87th Street
Milwaukee, WI 53226
Phone: 414-955-AOIP (2647)
Fax: 414-955-6690
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