32nd Annual International Conference of the IEEE EMBS

Buenos Aires, Argentina, August 31 - September 4, 2010

An Open Data Mining Framework for the Analysis of Medical

Images: Application on Obstructive Nephropathy Microscopy
Images
Charalampos Doukas, student Member, IEEE, Theodosis Goudas, Simon Fischer, Ingo Mierswa,
Aristotle Chatziioannou and Ilias Maglogiannis, Member, IEEE

Abstract—This paper presents an open image-mining
framework that provides access to tools and methods for the
characterization of medical images. Several image processing
and feature extraction operators have been implemented and
exposed through Web Services. Rapid-Miner, an open source
data mining system has been utilized for applying classification
operators and creating the essential processing workflows. The
proposed framework has been applied for the detection of
salient objects in Obstructive Nephropathy microscopy images.
Initial classification results are quite promising demonstrating
the feasibility of automated characterization of kidney biopsy
images.
I. INTRODUCTION
data mining of biomedical image data. The tools
implemented as Web Services can be directly integrated
workflow management platforms (e.g., TAVERNA [3]),
allowing their integration in several workflows
corresponding to different image processing pipelines.
Proper authentication and encryption mechanisms have been
utilized in order to guarantee the appropriate security. The
rest of the paper is organized as follows: Section 2 discusses
related work in image mining through Web Services.
Section 3 presents the tools and methods that enable the
functionality of the proposed platform, whereas the
architecture scheme is described in Section 4. Section 5
describes the Obstructive Nephropathy images

T he kidney is a multicellular, multistructure organ that is

responsible for a part of the complex process of blood’s
purification. Kidneys are being affected by many chronic
characterization process followed by initial evaluation
results in Section 6. Finally, Section 7 concludes the paper.

diseases, like Obstructive Nephropathy [1], which is the

main cause of renal failure. It is caused by obstruction of the
urinary tract, with hydronephrosis, which is dilation of the
renal pelvis and calyses resulting from obstruction to flow of
urine. Considering that Obstructive Nephropathy is not a
rare disease ([1]), an auto detection of the pathogenic areas
on a kidney biopsy image is very useful, especially in such
cases where the discrimination of healthy versus pathogenic
biopsy samples is quite difficult and complex (see Fig. 1).
The automated characterization of such images requires
proper preprocessing, (e.g., image enhancement, color
processing), feature extraction and classification. Nowadays
the trend in image processing and software engineering in
general is towards the development of algorithms and tools
that provide each one of these functions individually [2],
especially in form of Web Services, a technology that
enables developers to programmatically access
heterogeneous, distributed resources, providing easier
integration and interoperability between data and
applications. This paper presents an open framework based
on Web Services that provides access to complete tools for
Manuscript received April 1, 2010. This work is partly funded by the EU
via the e-LICO FP7 Collaborative Project (grant agreement 231519).
C. Doukas is with the University of the Aegean, Samos, Greece (e-mail:
doukas@aegean.gr). T. Goudas and I. Maglogiannis are with the University
of Central Greece, Lamia, Greece (e-mail: {goudas, imaglo}@ucg.gr). S.
Fischer and I. Mierswa are with Rapid-I GmbH (e-mail: {fischer,
ingo.mierswa}@rapid-i.com). A. Chatziioannou is with the National
Hellenic Research Foundation, Athens, Greece (email: achatzi@eie.gr)
a) b)
Fig. 1. Samples of obstructive nephropathy images. a) healthy biopsy
sample, b) pathogenic biopsy sample.
II. RELATED WORK
Despite the great impact of the Web Services in the
development and deployment of web applications, the
exploitation of the latter in the domain of biomedical data
mining is still quite narrowed. Only a few systems exist in
the literature that utilize Web Services in order to provide
functionality and access to computational resources for
processing, annotating and mining biomedical data and
especially medical images. The MIAKT system [4] provides
knowledge management of data generated by screening
processes and means for medical staff to investigate,
annotate, and analyze the data using web and GRID
services. In [5], authors have proposed a model for
implementing SOA (Service Oriented Architecture) based
image processing systems. The proposed architecture
consists of a programming model, a service model and a
messaging model. The authors focused on the concept of
service. The INBIOMED platform [6] is a Web Services

978-1-4244-4124-2/10/$25.00 ©2010 IEEE 4108

oriented architecture that provides a framework for sharing
resources and medical image processing algorithms. The
Web Services integrated into the platform provide
morphological operators and filters (e.g., erosion, dilation,
opening, closing) and segmentation methods.
The aforementioned works focus mostly on the provision
of specific functionalities for analyzing and processing
medical images of a narrowed range of modalities through
Web Services. To the best of our knowledge, there is no
work that enables the mining of biomedical images based on
a number of tools and frameworks providing complete
functionality through a single Web Service framework. The
major benefits of this approach can be summarized into the
following:
 Open access to biomedical image mining
functionality without specific requirements
 Total interoperability
 Provision of a complete framework.
 Single access point
 Image mining consistency and reliability
III. TOOLS AND METHODS
This section provides more details regarding the tools and
methods utilized for developing the presented image mining
framework.
A. Image Acquisition and Processing
The following aspects of image processing are considered:
 Acquisition. The framework provides support for the
acquisition, sampling and writing of image files,
complete program control and easy integration into
image-enabled applications that utilize databases.
 Transformations. It includes functions for transform an
image from space to frequency dimension (Fourier,
DCT) and wavelet transforms.
 Image Enhancement. Functionalities for image
enhancement such as subtraction, background
correction, denoising, smoothing, spatial and median
filtering, histogram equalization etc., are provided.
 Color Processing. It refers to pixel based processing that
will allow users to gather colour information (i.e. the
counting of the number of unique colors within an
image, or finding the dominant color are particularly
useful functions as it enables one analyze an image).
 Image Analysis and Feature Extraction. The toolbox
supports the extraction of the produced quantitative
features in XML files that may be directly stored into a
database for further processing and exploitation (e.g.,
classification using the Rapid Miner tool).
B. Image Mining through Web Services & Secure Access
Web Services are emerging as a promising technology to
build distributed applications. It is an implementation of
SOA [7] that supports the concept of loosely-coupled, open-
standard, language - and platform-independent systems. The
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loosely-coupled features allow service providers to modify
backend functions while maintaining the same interface to
clients. Web Services are accessed through the
HTTP/HTTPS protocols and utilize XML (eXtendible
Markup Language) for data exchange. This in turn implies
that Web Services are independent of platform,
programming language, tool and network infrastructure.
Services can be assembled and composed in such a way to
foster the reuse of existing back-end infrastructure. The WS-
Security kit (Rampart) [8] has been utilized for user
authentication. WS-Security is a standard for adding security
to SOAP Web Service message exchanges. It uses a SOAP
message-header element to attach the security information to
messages, in the form of tokens conveying different types of
claims (which can include names, identities, keys, groups,
privileges, capabilities, etc.) along with encryption and
digital-signature information. On top of the WS-Security kit,
the SSL [9] protocol has been used for the proper encryption
of the data during transmission between the service
consumer and the Web Service itself.
C. The Rapid-Miner Classification and Workflow
Management Tool
RapidMiner [13] is a flexible, modular, and extensible
data mining and data processing solution. Being an open
source project it is available to the scientific community and
has a large user base. Written entirely in Java it provides an
open API and can be easily integrated into any existing
application. In its standard version, RapidMiner comes with
hundreds of operators for machine learning, data
manipulation, filtering, format conversion, etc. As of version
5.0, the user interface and process execution engine has been
completely rewritten as a generic workflow execution
engine. Based on this, a set of new operators that integrate
transparently with the Web Services presented in the
preceding section have been developed. Using these
operators, it is possible to design data mining workflows that
connect seamlessly to the image mining tools described
above (see Fig. 3). The image mining extension
encompasses the following (groups of) operators:
List Images: This operator simply lists all image files
found in a particular directory.
Upload Images: The listed images are uploaded to the
image mining server, and a reference to the images is
obtained and stored. Subsequently, only this reference is
used and no intermediate up- or download of image data is
necessary.
Visualize Image: If desired, intermediate results can be
visualized within RapidMiner. This requires the download
of the processed images.
Image Transformation: Using the image references,
various image transformation algorithms are performed. The
transformed images are stored on the server.
Feature Extraction: Using image references, various
features features can be extracted and transformed into a The GLCM is a tabulation of how often different
tabular format which can be further used by RapidMiner for combinations of pixels brightness values (grey
data mining and processing. levels) occur in an image.
The groups of image transformation and feature i = the row number
extraction operators constitute the most relevant part. Due to j = the column number
self-description methods of the Web Service, RapidMiner is Pi,j = the element i, j of the normalized symmetrical
able to detect the set of provided algorithms automatically. GLCM
N 1
(1)
Hence, new image mining algorithms can be deployed ASM   iP 2
i, j
automatically without a need to update the RapidMiner i, j  0

components. Whereas RapidMiner is not aware of image  The Contrast, which gives a measure of how sharp
files, formats, etc., the image mining operators can be the structural variations in the image are.
n 1
combined flexibly to transform images into a tabular format C ontrast   Pi j ( i  j ) 2 (2)
well-suited for data mining and further processing. i, j0

 The Correlation, which is a measure of grey – level

IV. THE FRAMEWORK ARCHITECTURE linear dependency of the image’s segment.
n 1
(3)
The proposed framework is the based on the services- Correlation  P ij
( i   )( j   )
2
oriented architecture model as illustrated in Fig. 2. The main i, j0

component is the Image Processing Web Services Core that  The Inverse Difference Moment, which gives a
hosts all the functionality exposed to the client measure of the local homogeneity of the segment of
communication through SOAP messages and the the image.
HTTP/HTTPS protocol. Appropriate classes and functions ID M    1
1 ( i  j )2
Pi j (4)
implement the aforementioned functionality utilizing any i j

essential application programming interfaces (APIs) that  The Entropy, which is a measurement of randomness
provide access to advanced functionality (e.g., data Entropy    (5)
management, image processing, etc.) or to data repositories i
P j
ij  log( Pij )

and computational resources. The Web Services Core is

The above features have been selected as the most
hosted by an appropriate service container (i.e., usually an
appropriate in order to characterize and classify complex
application server). The latter usually resides among with
biomedical images, like the kidney biopsy images ([10],
additional resources (e.g., databases) in the framework
[12]. All processing steps are available as Web Service
container (physically can be a framework server). The
operators and can be inserted into the RapidMiner tool for
communication with the RapidMiner tool is performed
creating an automated workflow procedure.
through SOAP calls. This type of architecture is modular
and allows the easy integration of new services. B. Data Classification
The features described in previous section are obtained
through the appropriate workflow process designed and
V. SALIENT OBJECTS DETECTION IN OBSTRUCTIVE implemented in RapidMiner. Classification has been
NEPHROPATHY IMAGES performed using the k-Nearest Neighbor, the Naïve Bayes
and the Support Vector Machines (SVM) ([11]) classifiers.
A. Image Processing and Feature Extraction
Afterwards, ten-fold cross validation has been applied for
The characterization of obstructive nephropathy images evaluation purposes.
requires initially appropriate image processing and feature
extraction. Images are firstly enhanced by histogram
equalization and then converted to 8-bit. A segmentation
window of 40x40 pixels is applied for gridifying the initial
image into smaller parts. This step is performed in order to
increase the resolution of the dataset. Texture analysis
follows by calculating features like:
 The Mean, which gives the average value of the
segment’s pixels, along with the Standard
Deviation, which gives the value of the dispersion
of the values around the Mean.
 The Angular Second Moment (ASM), which gives a
measurement related to orderliness. ASM is
calculated using the Grey Level Co-occurrence Fig. 2. Illustration of the Framework Architecture
Matrix (GLCM) of the segment of the specific ROI.

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Fig. 3. Screenshot of the RapidMiner [13] interface illustrating a workflow
for processing, feature extraction and classification of Obstructive
Nephropathy Images.
VI. INITIAL EVALUATION RESULTS
In order to evaluate the accuracy of the image mining
framework for the characterization of obstructive
nephropathy images, an initial dataset of 6 Kidney biopsy
images has been utilized. The images have been provided by
INSERM (France). They have been obtained from healthy
and pathogenic kidney biopsies of mice, and have been
treated following Masson's trichrome staining technique in
order to disclose the most important structures (see Fig. 4).
A magnification of 200, aperture of 0.5, 10 ms exposition
and gain of 1.0 have been used as shooting settings. In order
to overcome the issue with the small dataset, the images
have been gridified (See Section V) resulting into a quite
larger dataset.
After applying the aforementioned image processing and
the k – Nearest Neighbor classifier, 260 over 283 non-
pathogenic Glomerulus (see Fig. 4) have been successfully
recognized (i.e. 91,87% accuracy) , whereas all pathogenic
Glomerulus were successfully classified.
Fig. 4. Annotation of important structures that determine pathogenesis in a
Kidney biopsy image. Strong line: Glomerulus, Dashed line: Tubulus
The Bayesian classifier achieved 67,82% accuracy in
predicting pathogenic areas. SVM have reached an accuracy
of 76,87%, in addition to the fact that all non-pathogenic
Glomerulus were successfully predicted.
VII. CONCLUSION
This paper has presented an open image mining
framework for the characterization of Obstructive
Nephropathy images. It is based on image processing and
feature extraction operators available as Web Services and
their integration in RapidMiner, an open data mining
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workflow tool. The framework enables experts to utilize
image mining techniques without any requirements for
specific image processing or data mining knowledge. Initial
evaluation results are quite promising. Future work includes
more extensive evaluation of the platform using new
datasets.
ACKNOWLEDGMENT
This work is funded by Information Society Technology
program of the European Commission “e-Laboratory for
Interdisciplinary Collaborative Research in Data Mining and
Data-Intensive Sciences (e-LICO)” (IST-2007.4.4-231519).
Authors would also like to thank Joost Schanstra and Julie
Klein from INSERM for the provision and annotation of the
biopsy images.
REFERENCES
[1] Klahr S, “Obstructive nephropathy”, Internal medicine, vol. 39, no 5.,
2000, pp. 355-361.
[2] Biological Web Services, June 2009, available online at:
http://maurobio.infobio.net/bws/biows.htm.
[3] Tom Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin
Senger, Mark Greenwood, Tim Carver, Kevin Glover, Matthew R.
Pocock, Anil Wipat and Peter Li, “Taverna: a tool for the composition
and enactment of bioinformatics workflows”, Bioinformatics, vol. 20,
no. 17, pp. 3045-3054, June 2004.
[4] Shadbolt, N. Lewis, P., Dasmahapatra S., Dupplaw D., Hu B. and
Lewis H., “MIAKT: Combining Grid and Web Services for
Collaborative Medical Decision Making”, In Proc. of AHM2004 UK
eScience All Hands Meeting, September 2004, Nottingham, UK.
[5] Todica V., Vaida M.F., “SOA-based medical image processing
platform”, in Proc. of IEEE International Conference on Automation,
Quality and Testing, Robotics, 2008, vol. 1, pp. 398-403, May 2008.
[6] D. Perez, J. Crespo, A. Anguita, J. Ordonez, J. Dorado, G. Bueno, V.
Feliu, A. Estruch, J. Heredia, “Biomedical Image Processing
integration through INBIOMED: A Web Services-based Platform”,
presented at the 6th International Symposium on Biological and
Medical Data Analysis (ISBMDA 2005).
[7] Newcomer, Eric; Lomow, Greg (2005). Understanding SOA with Web
Services. Addison Wesley. ISBN 0-321-18086-0.
[8] Kyle Gabhart, “Secure, Reliable Web Services with Apache”,
available online at: http://www.xml.com/pub/a/2007/05/02/sure-
reliable-web-services-with-apache.html.
[9] The OpenSSL Project, information available online at:
http://www.openssl.org/.
[10] Ilias Maglogiannis, Charalampos Doukas, “Overview of Advanced
Computer Vision Systems for Skin Lesions Characterization”, IEEE
Transactions on Information Technology in Biomedicine, vol 13, no 5,
pp. 721-733, Sept. 2009, DOI: 10.1109/TITB.2009.2017529..
[11] I. Maglogiannis, E. Zafiropoulos: “Utilizing Support Vector Machines
for the Characterization of Digital Medical Images” BMC Medical
Informatics and Decision Making 2004.
[12] Haralick M et al, “Textural Features for Image Classification”, IEEE
Transactions on systems man and cybernetics Vol. SMC-3 pp. 610-
621, 1973.
[13] Miersw Ingo, Wurst Michae, Klinkenberg Ralf, Scholz Martin and
Euler Timm. “YALE: Rapid Prototyping for Complex Data Mining
Tasks”, in Proceedings of the 12th ACM SIGKDD International
Conference on Knowledge Discovery and Data Mining (KDD-06),
2006.