Automatic Retinal Image Registration Using fully
Connected Vascular Tree
Janabai Parekar, Prasanna Porwal and Manesh Kokare
Center of Excellence in Signal and Image Processing
Shri Guru Gobind Singhji Institute of Engineering and Technology
Vishnupuri, Nanded (M.S.), India
{parekarjanabai14-15, porwalprasanna, mbkokare}@sggs.ac.in
Abstract—Retinal image registration plays very important role
in medical imaging, as it combines the information of different
field of view images and temporal images. This paper presents the
novel method for retinal image registration based on bifurcation
structure matching. In proposed method, segmentation is based
on the multi-scale ridge detection, and the preprocessing steps
used to avoid false detection of vessels. Also, Dijkstra’s algorithm
is used to get a fully connected vascular tree. A novel technique is
proposed for removing the false correspondence. This method is
invariant to translation, rotation and scaling since feature vector
contains normalized lengths and angles. The registered image is
visually good as well as experimental performance shows very
good results.
Index Terms—Retinal image registration, Vessel segmentation,
Bifurcation structure, Transformation model.
I. I NTRODUCTION
Retinal imaging has significantly grown in the field of
ophthalmology in last few decades. Fundus photography is
the non-invasive method, which takes direct images of the
retina. Current research is focused on automatic early detection
of diabetic retinopathy using fundus photographs. Automated
retinal image registration is an important step in diabetic
retinopathy for treatment evaluation. An accurate registration
helps to diagnose the progression of diseases. Hence, this
paper focusses on retinal image registration. Image registration
is defined as aligning two or more images of the same scene
taken at a different time with different camera parameter. In
this process, one image is taken as a reference image or fixed
image. The transformation parameter of another image (target
image) with respect to the reference image is found and these
two images are aligned.
Broadly, retinal image registration belongs to two cate-
gories. First category is intensity based and second is feature
based [1]. The intensity-based methods depend on gradient and
cross-correlation, intensity differences and shared information
of images. Kim et al. [2] proposed a method which is insensi-
tive to outliers. Matsopoulos et al. [3] used simulated annealing
and genetic algorithms to improve the object function based
on the intensity differences of the segmented retinal images.
Intensity-based method needs whole image information for
registration. If quality of image is a low or overlapping area
in concerned images are lesser, then intensity based method
might fail to register images.
Feature-based method uses features of image as vascular
bifurcation points, trifurcation points, whole vascular tree, and
other feature of image. Steward et al. [4] used vascular bifur-
cation points and crossing points as landmark points. Yang et
al. [5] proposed Generalized Dual-Bootstrap Iterative closest
Point (GDB-ICP) method based on SIFT key points. Feature-
based registration methods also fail to align low-quality retinal
images. Though there are different methods available for
retinal image registration, it is still very challenging to find
pixel correspondence. These challenges are, firstly there is very
small overlapping area between the images. Secondly, retinal
images having bleeding or tumor tissue reduce the number
of detectable bifurcation points or may inhibit their correct
segmentation. Thirdly, contrast and intensity distribution of
images create problems for feature based and intensity based
methods. Finally, a difference of intensity between the vessel
center line and vessel edges, which causes false detection of
vessels.
To solve above challenges, we have proposed a novel
method using bifurcation structure which uses ordered statistic
filter for processing, multi-scale ridge detection for vessel
segmentation and Dijkstra’s algorithm for joining disconnected
vessels. This paper is organized as follows, Section II explains
the proposed method. In section III, experimental results are
given, finally section IV concludes this paper.
II. P ROPOSED M ETHODOLOGY
Fig. 1 shows proposed methodology. The retinal vessel has
different width and orientation, hence segmentation is not
possible using a single scale. So multi-scale ridge detector
is used to segment vessels of different widths. In proposed
method images are resized to 858×570 in order to reduce
computational complexity.
A. Preprocessing of Retinal Images
Retinal blood vessel segmentation is challenging due to
low contrast between blood vessels and retinal background
hence, green channel is used for segmentation [6]. Vessels
in retinal images are darker in nature, but the center line
of some vessels has high-intensity compared to their edges.
Due to this, the output of segmentation contains edges of
vessels. To remove this effect ordered statistic filter is used.
A minimum and maximum ordered filter is used successively.

Fig. 1. Flow chart of proposed method.
(a) (b)
Fig. 2. Output of pre-processing : (a) Original image, (b) Image after
processing.
Minimum filtering blurs the vessel and fills the center line
of vessels, whereas maximum filtering is used to sharpen the
vessel boundary. These preprocessing steps improve contrast
between vessels and background as well as remove edge
detection effect. Fig. 2 show the effect of preprocessing on
the retinal image.
B. Vessel segmentation
In order to proceed for registration, we need to segment
retinal vessels first. As blood vessels are elongated structures
of different diameters and orientation, vessel segmentation
is mentioned as ridge detection [7]. The dark line detecting
property of hessian matrix is used to detect these ridges. As
single-scale ridge detectors detect only specific width of a
vessel so four different scales are used to detect vessels of
radii 1 to 7 pixels. An eigenvalues of the hessian matrix for
image I are calculated as:
 
I Ixy
H = xx (1)
Ixy Iyy
Ixx + Iyy ± α
λ1 , λ2 = (2)
2
Where, Ixx , Iyy are second order derivative of image in x,
y directions respectively and
q
α = (Ixx − Iyy )2 + 4Ixy2 (3)
The response is pixel-wise maximum over different scales.
1) Non-maximum suppression: The output of the previous
step is a gray scale image having a maximum response to
vessels. To obtain vessel centerline, pixels around vessel center
line have to suppress. To decide it, an image is scanned along
the direction of the gradient, and if the pixel is not local
maxima then it is set as zero. After this step, a threshold is set
and the image is converted to a binary image. Morphological
thinning is applied on this image for getting single pixel width
vessels.
2) Noise Removal: Result of non-maximum suppression
contains false and disconnected vessels. These false vessels
are removed using following steps.
Step I: Determine the connected component.
Step II: Compute the area of each component.
Step III: Remove small object.
To find connected component eight neighborhood connectivity
is used. The component having an area less than 20 pixels are
removed, which is usually false vessels. Fig. 3(b) shows the
output of vessel segmentation after noise removal.
3) Connecting Vessel: Noise removed image still contains
some disconnected vessels. These vessels should connect such
that it must look natural. Dijkstra’s single source shortest path
algorithm is used to find the shortest path from source to every
other vertex. Let G = (V, E) is a given graph, where V = vi
is set of vertices, and E = wij is weight of arc from vi to
vj . Time complexity of Dijkstra’s algorithm [8] having M
nodes is O(M 2 ) . We label each disconnected vessel as one
object. Suppose there are k numbers of disconnected vessels,
so resultant image is formed by combining these isolated
objects and background as:
Ω = Ω0 ∪ Ω1 ∪ ... ∪ Ωk ; ∀i 6= j, Ωi ∩ Ωj = Ø (4)
Here Ω0 is background and Ω1 ...Ωk is an isolated vessel in
foreground. We define the graph in which every image pixel
acts as vertex. If two vertices are four or eight neighborhoods
of each other then they are connected by an arc directed from
vertex vi to vj . The distance between such vertices is given
by weight of an arc from vi to vj as:

0; vj ∈ Ω1 ∪ ... ∪ Ωk
wij = (5)
h(vj ); vj ∈ Ω0
Here we have set wij = 0 if vj belongs to foreground,
wij = h(vj ) if vj belongs to background. In order to find
the shortest path for foreground pixel, weight for pixels
belongs to the foreground is kept to zero. The term h(vj )
depends upon response of ridge detector. Ridge detector has a
maximum response at the center of the vessel. If the response
 (a) (b)
Fig. 3. Output of vessel segmentation. (a) Color retinal image from
DRIVE database, (b) initial segmentation results, (c) fully connected
vascular tree.
is maximized, then the weight of the arc should be minimum.
Hence h(vj ) is calculated as
f (vj )
h(vj ) = 1 −
max[f ]
Where f (vj ) is the output of ridge detector at given vertex
and h(vj ) has normalized in range [0, 1]. The shortest path
follows the pixel having a maximum ridge response. We have
used 8-neighborhood connectivity for defining a graph. A
single source is selected randomly from largest ridge region.
This algorithm finds the shortest path from the source to every
other vertex simultaneously. After finding shortest path fully
connected vessel tree is formed by joining these paths. Fig.
3(c) shows fully connected vascular tree.
C. Image Registration
Proposed method of retinal image registration is based on
feature matching hence bifurcation structure of blood vessels
is used for finding features. The process of forming feature
vector is described in the following section.
1) Matching of Bifurcation Structure: Bifurcation structure
is composed of one center bifurcation point and is surrounded
by three neighbors [9]. Fig. 4 shows the bifurcation structure
showing features. Feature vector should be robust to trans-
lation, rotation, scaling, distortion and other transformation.
Hence we have normalized the feature vector. Bifurcation
structure consists of four bifurcation points, hence the feature
vector is a combination of a characteristic of these four points.
Feature vector of each bifurcation structure is given as:
V = [lengths, angles]
V = [l1 , l2 , l3 , θ1 , θ2 , θ3 , θ4 , θ5 , θ6 , θ7 , θ8 , θ9 , θ10 , θ11 , θ12 ]
Where li and θi are the normalized lengths and angles
respectively.
li =ith branch length/sum[length1, length2, length3]
θi =ith angle in degree/360o
Feature vector V is arranged in ascending order of lengths
and angles. Let P and Q denote feature group of two given
images having N1 and N2 bifurcation structures, respectively.
(c)
Fig. 4. The bifurcation structure and its features.
Degree of similarity Si,j for bifurcation structure pair is given
as
Si,j = d(pi , qj ) (9)
Where pi and qj are ith and jth bifurcation structure in two
(6)
images and d is the simple distance between two feature vec-
tors. Here dummy bifurcation, crossover and terminal points
are discarded as these points are more error-prone.
2) Verification of Matched Pairs: Verification of matched
pair is very important to avoid false correspondence. Minimum
correspondence points required for linear and similarity trans-
formation are 2 and 3 pairs respectively. In our method single
matched bifurcation structure give four point pairs. Therefore,
one matched bifurcation structure is enough for registration.
Matched pairs are verified as:
err(ij, mn) = d(M (pi , qj ), M (pm , qn )) (10)
Here M (pi , qj ) and M (pm , qn ) are transformation models
estimated from matched pairs pi and qj , pm and qn respec-
tively. If matched pairs are correct, then the difference between
transformation models of matched pairs should be minimum.
Matched pairs having more difference in transformation model
is discarded in this step.
3) Validation of Registered Images: Images of different
field of view of the same retina contain different overlapping
area. A number of matched bifurcation structure varies accord-
ing to the overlapping area. Images with more overlapping area
are having more number of structure matches found. There
is a need to verify that how many structures are accurately
matched, since for estimating the transformation model true
correspondence is required. This is done by verifying the trans-
(7) formed image. In registration, one image act as a reference
image and we find transformed second image using n best-
matched structure. Before computing overlapping pixels, both
images are dilated using the disc structuring element of size
(8) 3×3 to compensate the very small registration error.
IfTinal = max[(Iref ⊕ S) × (InT ⊕ S)] (11)
Iregistered = Iref + IfTinal (12)
Where, Iref is vessel segmented reference image, IT is
vessel segmented transformed second image, S is structuring
element and n is a number of bifurcation structure used for
 TABLE I. E XPERIMENTAL R ESULTS
Method Mean Err (pixels) Std. Devi.(pixels)
GDB-ICP 3.505 2.789
Proposed method 1.785 0.974
finding transformation model. Value of n for which maximum
overlapping obtain is used to get transformation of image.
III. E XPERIMENTAL R ESULTS
Presently there is no public dataset of retinal images avail-
able for retinal image registration. We have done experimenta-
tion using proposed method on a private dataset collected from
Sushrusha Hospital, Nanded. Dataset consists of a different
set of images of individual patients covering different fields
of view images specially collected for this research work. We
have registered images having different pathologies, different
overlapping areas and low contrast.
Retinal images first segmented using ridge based vessel
segmentation and then fully connected vessel tree are obtained
using a Dijkstra’s algorithm. Proposed retinal image registra-
tion method is applied to fully segmented retinal vascular tree.
We have tried a different transformation model and observed
that similarity transformation model gives the best result. In
Fig. 5, a rectangle marks matched bifurcation point. Here four
best-matched bifurcation structure is shown. Here images are
of size 858×570.
Performance of proposed retinal image registration is eval-
uated using mean and standard deviation of registration error
[1]. Registration error of image pair is given as the mean
Euclidian distance between control points of the reference
image and the transformed image. We have manually selected
8 to 20 points of reference image which is also present in the
second image. These points are bifurcation points as it maps
the whole retina and localized accurately. We have verified
the proposed method using six image pairs by comparing its
result with GDB-ICP algorithm [5] given in Table I.
IV. C ONCLUSION
Proposed retinal image registration method uses vascular
structure to find the correspondence. This method is robust to
translation, rotation, scaling and intensity of the images. Reg-
istered image visually looks very good and also the registration
error is very small. Image preprocessing improves contrast
between vessels and background which improves segmenta-
tion. Proposed method removes false matching of structure. A
feature based registration method is proposed which uses the
bifurcation structure for finding the correspondence. Similarity
transformation gives the best result.
ACKNOWLEDGMENT
The authors would like to express gratitude toward Dr.
Girish Deshmukh, Susrusha Hospital, Nanded for support, giv-
ing clinical insight and sharing retinal images for our research
work. We would also like to thank Technical Education Quality
Improvement Program (TEQIP II) for supporting our project.
(a) (b)
(c) (d)
(e) (f)
Fig. 5. Result of registration. (a)Reference retinal image, (b)Vascular
tree of (a) with matched bifurcation structures, (c)Second retinal
image of same retina, (d)Vascular tree of (c) with matched bifurcation
structures, (e)Mosaic retinal image and (f)Mosaic vescular image.
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