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            <title>Image Acquisition &amp; Processing Routines for Damaged Manuscripts</title>
            <author><name>Melanie Gau</name>
               <address>
               <addrLine>Institute of Slavic Studies</addrLine>
               <addrLine>University of Vienna</addrLine>
               <addrLine><ref target="mailto:melanie.gau@univie.ac.at">melanie.gau@univie.ac.at</ref></addrLine></address>
            </author>
            <author>
               <name>Heinz Miklas</name>
               <address>
               <addrLine>Institute of Slavic Studies</addrLine>
               <addrLine>University of Vienna</addrLine>
               <addrLine><ref target="mailto:heinz.miklas@univie.ac.at">heinz.miklas@univie.ac.at</ref></addrLine></address>
            </author>
            <author>
               <name>Martin Lettner</name>
               <address>
                  <addrLine>Computer Vision Lab</addrLine>
               <addrLine>Institute of Computer Aided Automation</addrLine>
               <addrLine>Vienna University of Technology</addrLine>
               <addrLine><ref target="mailto:lettner@caa.tuwien.ac.at">lettner@caa.tuwien.ac.at</ref></addrLine></address>
            </author>
            <author>
               <name>Robert Sablatnig</name>
               <address>
                  <addrLine>Computer Vision Lab</addrLine>
               <addrLine>Institute of Computer Aided Automation</addrLine>
               <addrLine>Vienna University of Technology</addrLine>
               <addrLine><ref target="mailto:sab@caa.tuwien.ac.at">sab@caa.tuwien.ac.at</ref></addrLine></address>
            </author>
            <editor role="acceptingeditor">
               <name>Malte Rehbein</name>
               <address> 
                        <addrLine>Universität Würzburg</addrLine>
                    </address>
            </editor>
            <editor role="recommendingreader">
               <name>Ségolène M. Tarte</name>
               <address><addrLine>Oxford e-Research Centre</addrLine>
                  </address>
            </editor>
            <editor role="recommendingreader">
               <name>John Keating</name>
               <address> 
               <addrLine>National University of Ireland, Maynooth</addrLine> 
               </address></editor>
         </titleStmt>
         <publicationStmt>
            <publisher>Digital Medievalist, University of Lethbridge</publisher>
            <pubPlace>Lethbridge AB, Canada T1K 3M4 </pubPlace>
            <availability>
               <p>© Melanie Gau, Heinz Miklas, Martin Lettner, and Robert Sablatnig, 2010. Creative
                  Commons Attribution-NonCommercial licence</p>
            </availability>
            <date n="received" when="2009-11-09"/>
            <date n="revised" when="2010-05-17"/>
            <date n="published" when="2011-03-03"/>
         </publicationStmt>
         <seriesStmt>
            <title>Digital Medievalist</title>
            <idno type="issue">6</idno>
            <idno type="date">2010</idno>
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               <term type="DMType">Article</term>
               <term type="keyword">Image Acquisition</term>
               <term type="keyword">Processing</term>
               <term type="keyword">Manuscripts</term>
               <term type="keyword">Codicology</term>
               <term type="keyword">Palaeography</term>
               <term type="keyword">Multi-Spectral Imaging</term>
               <term type="keyword">Foreground-Background Separation</term>
               <term type="keyword">Graphemic Character Segmentation</term>
               <term type="keyword">Damaged Manuscripts</term>
               <term type="keyword">Palimpsests</term>
               <term type="keyword">Digital Palaeography</term>
            </keywords>
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      <front>
         <argument n="abstract">
            <p>This paper presents an overview of data acquisition and processing procedures of an
               interdisciplinary project of philologists and image processing experts aiming at the
               decipherment and reconstruction of damaged manuscripts. The digital raw image data
               was acquired via multi-spectral imaging. As a preparatory step we developed a method
               of foreground-background separation (binarisation) especially designed for
               multi-spectral images of degraded documents. On the basis of the binarised images
               further applications were developed: an automatic character decomposition and
               primitive extraction dissects the scriptural elements into analysable pieces that are
               necessary for palaeographic and graphemic analyses, writing tool recognition, text
               restoration, and optical character recognition. The results of the relevant
               procedures can be stored and interrogated in a database application. Furthermore, a
               semi-automatic page layout analysis provides codicological information on latent page
               contents (script, ruling, decorations).</p>
         </argument>
         <argument n="acknowledgements">
            <p>This work was supported by the Austrian Science Foundation (<ref
                  target="http://www.fwf.ac.at/">www.fwf.ac.at</ref>) under grant № P19608-G12.</p>
         </argument>
      </front>
      <body>
         <div>
            <head xml:id="section1">Introduction</head>
            <p xml:id="gau.p0001">The handling of corrupted manuscripts poses new challenges to
               image acquisition and data editing. In the case of the project "Critical Edition of
               the New Sinaitic Glagolitic Euchology (Sacramentary) Fragments with the Aid of Modern
               Technologies" the data material consists of two parchment codices of the Old Church
               Slavonic canon dating from the eleventh century: the so-called <title level="m"
                  >Missale Sinaiticum</title> (Sin. slav. 5/N) and the new part of the <title
                  level="m">Euchologium Sinaiticum</title> (Sin. slav. 1/N). Both fragments belong
               to the complex of new findings from St. Catherine’s Monastery on Mount Sinai in 1975.
               They show extensive damage including faded or blurred ink, staining due to mould or
               humidity, degradation of the parchment (e.g. chipping, fragmentation and contortion
               of folia), and the rare phenomenon of chemical conversion of black into white ink.
               The manuscripts also partly contain palimpsest (re-written) folia.</p>
            <p xml:id="gau.p0002">For the decipherment and reconstruction of the texts mere
               philological means turned out to be insufficient (<ref target="#miklas2004">Miklas
                  2004</ref>), so in 2007 an interdisciplinary project of philologists (University
               of Vienna), computer scientists (image processing group PRIP, Vienna University of
               Technology) and material chemists (Vienna Academy of Fine Arts) was set up. The
               project has two major objectives: Research in technologies for the analysis and
               reconstruction of damaged manuscripts and the preparation of critical editions; the
               latter aim includes a paper edition with high quality facsimiles and data on the
               makeup of the manuscripts, as well as an electronic edition in the <title level="m"
                  >Manuscript</title> database (<ref target="#barnovforthcoming">Baranov
                  forthcoming</ref>). The interdisciplinary cooperation of philologists and image
               processing experts provided the unique opportunity to develop computer aided routines
               assisting the philological research of manuscripts.</p>
            <p xml:id="gau.p0003">The basis for the application of text reconstruction techniques is
               Multi-Spectral Imaging (MSI), which has proven to be a capable technique for the
               analysis and preservation of ancient documents (<ref
                  target="#eastonknowChristens-barry2003">Easton, Knox, et al. 2003</ref>).
               Originally utilized in remote sensing applications such as earth observation and
               region classification (<ref target="#richardsxiuping2005">Richards, Xiuping
                  2005</ref>), at the beginning of this millennium researchers started applying this
               approach also to the examination of historical documents. Especially images of the
               UltraViolet (UV) and InfraRed (IR) light ranges reveal additional information hidden
               to the human eye (<ref target="#Mairinger2003">Mairinger 2003</ref>). Applied to
               ancient manuscripts, Easton et al. (<ref target="#eastonknowChristens-barry2003"
                  >2003</ref>) were the first to capture and enhance the erased underscript of the
               famous Archimedes palimpsest with MSI methods. It became apparent that the
               application of spectral imaging can improve readability, especially of damaged
               manuscripts (<ref target="#rapantzikosbalas2005">Rapantzikos, Balas 2005</ref>), more
               than conventional colour imaging procedures. </p>
            <p xml:id="gau.p0004">On an expedition to Mount Sinai in 2007 we acquired a corpus of
               MSI data from approximately 150 folia from the relevant manuscripts. Nine spectral
               images were taken of each folio with a radiometric resolution of 12 bits and a
               spatial resolution of 565 dpi. The MSI acquisition system will be described in <ref
                  target="#section2">"Multispectral Image Acquisition," below</ref>.</p>
            <p xml:id="gau.p0005">However, high quality raw digital images alone are not sufficient
               for the decipherment of damaged manuscripts. In order to exploit the full range of
               information in the MSI data, further procedures are necessary. Particularly a robust
               foreground-background separation is essential for further image enhancement and both
               automated and manual investigations in codicology, palaeography and text
               reconstruction. To separate text from background we combine the spectral signature of
               the MSI data with the spatial characteristics of characters or strokes by
               incorporating a Markov Random Field (MRF) model (<ref target="#section3"
                  >"Foreground-Background Separation"</ref>).</p>
            <p xml:id="gau.p0006">In <ref target="#section4">"Further Project Applications"</ref> we
               will also discuss some further applications that have been developed in the course of
               the project: (1) For character decomposition and feature extraction (<ref
                  target="#section4.1">"Character Decomposition and Primitive Extraction"</ref>) the
               quality of the underlying binary input image is essential to achieve positive
               results. Here, the individual characters are thinned to a skeleton, dissected into
               their segments (primitives) and analysed according to criteria of linguistic
                  <term>graphetics</term> (script description). For further interpretation the
               results can be transferred to a database (<ref target="#section4.2">"Character
                  Database"</ref>). As the character features can also be analysed and inserted in
               the database manually, we are now able to compare and evaluate manual and
               computational script description. (2) The tool for layout analysis (<ref
                  target="#section4.3">"Layout Analysis"</ref>) supports codicological
               investigations such as ruling detection and script alignment (hanging or standing),
               the positioning of fragments, and the reconstruction of latent text material.</p>
            <p xml:id="gau.p0007">All applications are tailored especially for damaged historical
               manuscripts and prepare the ground for subsequent examinations, philological (e.g.
               layout interpretation, the creation of sample alphabets, script and scribe analyses)
               as well as technical procedures (e.g. optical character recognition and scribe
               identification).</p>
         </div>
         <div>
            <head xml:id="section2">Multispectral Image Acquisition</head>
            <p xml:id="gau.p0008">MSI applied in the spectral ranges from UV via VISible (VIS) up to
               the Near InfraRed (NIR) light range combines conventional imaging and spectrometry
               information of an object. The acquisition setup used for the Old Church Slavonic
                  <title level="m">Sinaitic Euchologies</title> consists of a digital colour camera
               and a scientific high resolution camera. Colour images and UV fluorescence images are
               captured with a Nikon D2Xs RGB camera providing images principally for visualisation
               purposes and the facsimile publications. For the multi-spectral images we use a
                  <term>Hamamatsu C9300-124</term> camera with a spectral sensitivity from UV to NIR
               (330nm-1000nm) and a resolution of 40002672 pixels. A filter wheel mounted in front
               of the camera selects different spectral images. <ref target="#figure1">Figure
                  1</ref> shows the alignment of the two cameras. </p>
            
               <figure xml:id="figure1">
                  <figDesc>Figure 1: Image Acquisition System</figDesc>
                  <graphic url="support/Fig1.png" height="300px"/>
               </figure>
            

            <p xml:id="gau.p0009">The setup yields a spatial resolution of 565 dpi for the
               multi-spectral images and a resolution of approximately 500 dpi for the conventional
               colour camera. Since every page is captured with both cameras, it is necessary to
               shift the folia from one camera to the other. To obtain multi-spectral images we use
               four band-pass (BP) filters with a peak of 450 nm (blue), 550 nm (green), 650 nm
               (red), 780 nm (NIR), two low-pass (LP) filters with a cut-off frequency of 400 nm (UV
               fluorescence) and 800 nm (IR reflectography), and a high-pass (HP) filter with a
               cut-off frequency of 400 nm to capture UV reflectography images. Using UV
               illumination for the UV reflectography and fluorescence, and VIS-NIR illumination for
               the other images we obtain nine different spectral images. The spectral transmittance
               of the filters is visualised in the electromagnetic spectrum in <ref
                  target="#figure2">Figure 2.</ref>
            </p>
            
               <figure xml:id="figure2">
                  <figDesc>Figure 2: Spectral Ranges of the Optical Filters</figDesc>
                  <graphic url="support/Fig2.png" height="400px"/>
               </figure>
            

            <p xml:id="gau.p0010">
               <ref target="#Table1">Table 1</ref> specifies the individual spectral images. The
               number beside the filter type specifies the selected wavelength in nm and the type of
               image can be seen in the annotation.</p>
            <table rend="boxed" xml:id="Table1">
               <head>Spectral Images for Hamamatsu (H) and Nikon (N) Camera</head>
               <row>
                  <cell>
                     <hi>Channel</hi>
                  </cell>
                  <cell>
                     <hi>Filter</hi>
                  </cell>
                  <cell>
                     <hi>Annotation</hi>
                  </cell>
               </row>
               <row>
                  <cell>H1</cell>
                  <cell>HP 400</cell>
                  <cell>UV reflectography</cell>
               </row>
               <row>
                  <cell>H2</cell>
                  <cell>LP 400</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>H3</cell>
                  <cell>BP 450</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>H4</cell>
                  <cell>BP 550</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>H5</cell>
                  <cell>BP 650</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>H6</cell>
                  <cell>BP 780</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>H7</cell>
                  <cell>LP 800</cell>
                  <cell>IR reflectography</cell>
               </row>
               <row>
                  <cell>H8</cell>
                  <cell>no filter</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>N1</cell>
                  <cell>RGB</cell>
                  <cell>VIS-IR</cell>
               </row>
               <row>
                  <cell>N2</cell>
                  <cell>RGB</cell>
                  <cell>UV fluorescence</cell>
               </row>
            </table>
            <p xml:id="gau.p0011">Due to the use of optical filters the images must be registered on
               one another before further processing (<ref target="#brauersschulteaach2008">Brauers,
                  Schulte, et al. 2008</ref>). The registration process used is described in Diem
               (2008). By the combination of several spectral bands (e.g. by principal component
               analysis) the readability could be considerably improved compared to the conventional
               RGB images (<ref
                  target="#miklasgaukleberdiemlettnervillsablatnigschreinermelcherhammerschmid2008"
                  >Miklas, Gau, et al. 2008</ref>).</p>
         </div>
         <div>
            <head xml:id="section3">Foreground-Background Separation</head>
            <p xml:id="gau.p0012">Since the beginning of computational historical document analysis
               researchers have been developing special methods for the analysis of degraded
               documents (<ref target="#gatospratikakisperantonis2004">Gatos, Pratikakis, et al.
                  2004</ref>). Contrary to previous studies which aim particularly at the
               enhancement of underwritten texts in palimpsest-manuscripts, we focus on the
               separation of text from background. For generating binary images from such ancient
               manuscripts, faded ink, mould stains, and the varying appearance of the text on
               different pages are the most challenging problems. Since independent component
               analysis methods are based on the assumption of the mutual independence of the
               sources (<ref target="#tonazzinibedinisalerno2004">Tonazzini, Bedini, et. al.
                  2004</ref>), these methods are not applicable for our purpose.</p>
            <div>
               <head xml:id="section3.1">Related Work and Overview</head>
               <p xml:id="gau.p0013">A large number of publications, competitions (<ref
                     target="#gatosntirogiannispratikakis2009">Gatos, Ntirogiannis, et al.
                     2009</ref>) and new applications are devoted to the subject of converting
                  document images into binary images and separating text from background. Overview
                  papers comparing different methods are given for instance in Gupta et al. (<ref
                     target="#guptajacobsongarcia2007">2007</ref>) or Leedham et al. (<ref
                     target="#leedhamyantakruhaditanmian2003">2003</ref>). In general, binarisation
                  algorithms for document image analysis can be divided into three main classes
                     (<ref target="#garainpaquetheutte2006">Garain, Paquet, et al. 2006</ref>):</p>
               <list type="unordered">
                  <item>global thresholding,</item>
                  <item>adaptive thresholding, or</item>
                  <item>clustering algorithms.</item>
               </list>
               <p xml:id="gau.p0014">Global and adaptive thresholding techniques use a threshold <hi
                     rend="italic">T</hi> to distinguish between foreground and background and are
                  therefore executed primarily on grey level images <hi rend="italic">I(i,j)</hi>.
                  The resulting black and white binary image <hi rend="italic">BW(i,j)</hi> is
                  defined as:</p>
               
                  <figure>
                     <graphic url="support/BW2.png" height="100px"/>
                  </figure>
               
               <p xml:id="gau.p00015">Clustering algorithms like <emph>k-</emph>means use the grey
                  level or colour to classify similar observations into foreground or background
                     (<ref target="#leydierbourgeoisemptoz2004">Leydier, et al. 2004</ref>).
                  Generating binary images from colour or multispectral images is still not
                  prevalent (<ref target="#garainpaquetheutte2006">Garain, et al. 2006</ref>).
                  Alternatively, in the simplest way, colour images are converted into grey level
                  images and then converted into binary images by thresholding.</p>
               <p xml:id="gau.p0016">In the case of old and degraded documents, local methods
                  outperform global ones. For instance, Sauvola and Pietikäinen (<ref
                     target="#sauvolapietikainen2000">2000</ref>) developed an adaptive document
                  image binarisation by determining a threshold for each pixel. Gatos et al. (<ref
                     target="#gatospratikakisperantonis2006">2006</ref>) developed an adaptive
                  degraded image binarisation algorithm following several distinctive steps: Wiener
                  filtering, a rough estimation of the foreground region, the calculation of the
                  background model, and finally post-processing methods like shrink and swell
                  filtering to improve the quality. Recently Moghaddam and Cheriet (<ref
                     target="#moghaddamcheriet2009">2009</ref>) proposed a method for the
                  restoration of single-sided low-quality document images based on a multi-level
                  classifier. This approach is designed for colour images of historical documents
                  and is based on connected component labelling to capture spatially linked pixels
                  of similar colour. Wolf and Doerman (<ref target="#wolfdoermann2002">2002</ref>)
                  use MRF models for the binarisation of low quality text. Their model for the
                  spatial relationship is defined on a neighbourhood of 4x4 pixel cliques. Cao and
                  Govindarayu (<ref target="#caogovindaraju2009">2009</ref>) use MRFs for the
                  binarisation of degraded handwritten forms where the spatial relations are
                  obtained from a training set of high quality binarised images and consist of 114
                  representatives of shared patches.</p>
               <p xml:id="gau.p0017">In contrast to the studies cited above we have developed an
                  algorithm for foreground-background segmentation operating on multispectral
                  images. Therefore we do not use threshold or clustering, but combine spectral and
                  spatial features.</p>
            </div>
            <div>
               <head xml:id="section3.2">MRF Based Foreground-Background Separation of MSI
                  Data</head>
               <p xml:id="gau.p0018">Our main idea for foreground-background separation is to
                  combine spatial and spectral features. Therefore we utilise an MRF model which
                  provides a probability theory for analysing spatial or contextual dependencies
                     (<ref target="#li2009">Li 2009</ref>). Emphasis on the combination of spatial
                  and spectral components is particularly important in the case of ancient documents
                  with varying textures (e.g. of the hair and flesh sides of parchment). Therefore,
                  we include the visual nature of characters by means of stroke features. The only
                  parameter we need is the mean stroke width, which can also be evaluated
                  automatically (<ref target="#pervouchineleedhammelikhov2005">Pervouchine, Leedham,
                     et al. 2005</ref>).</p>
               <p xml:id="gau.p0019">The MRF model (<ref target="#li2009">Li 2009</ref>) is commonly
                  represented by an energy function <hi rend="italic">E(x)</hi> on a regular lattice
                     <hi rend="italic">S</hi>
                  <figure>
                     <graphic url="support/E(X)_2.png" height="100px"/>
                  </figure> where <hi rend="italic">&#x03a8;<hi rend="sub">i</hi>(x<hi rend="sub"
                        >i</hi>)</hi>
                  <!--<graphic url="support/psi_i.png" rend="inline"/>--> are the data costs, i.e.,
                  the costs assigning the label <hi rend="italics">x<hi rend="sub"
                  >i</hi></hi><!--<graphic
                     url="support/GRAPHIC-MISSING-HERE" rend="inline"/>-->
                  to pixel <hi rend="italic">i&#x2208;S</hi>
                  <!--<graphic
                     url="support/ies.png" rend="inline"/>-->. The
                  second term <hi rend="italic">&#x03a8;<hi rend="sub">i,j</hi>(x<hi rend="sub"
                        >i</hi>,x<hi rend="sub"
                  >j</hi>)</hi><!--<graphic url="support/GRAPHIC-MISSING-HERE" rend="inline"/>--> is
                  the cost of assigning labels <hi rend="italic">x<hi rend="sub">i</hi></hi>
                  <!--<graphic url="support/GRAPHIC-MISSING-HERE" rend="inline"
                  />-->
                  and <hi rend="italic">x<hi rend="sub"
                  >j</hi></hi><!--<graphic url="support/x_j.png" rend="inline"/>--> (belonging to a
                  clique <hi rend="italic">C</hi>) to two neighbouring pixels, where <hi
                     rend="italic">β</hi> is a weighting parameter controlling the prior. The
                  labelling <hi rend="italic">x</hi> with minimum energy <hi rend="italic">E(x)</hi>
                  is the optimal solution and can be found via energy minimization methods like
                  belief propagation (<ref target="#freemanpasztorcarmichael2000">Freeman, Pasztor,
                     et al. 2000</ref>) or Iterated Conditional Modes (ICM) (<ref
                     target="#besag1986">Besag 1986</ref>). </p>
               <p xml:id="gau.p0020">The prior model <hi rend="italic">&#x03a8;<hi rend="sub"
                        >i,j</hi>(x<hi rend="sub">i</hi>,x<hi rend="sub"
                  >j</hi>)</hi><!--<graphic url="support/GRAPHIC-MISSING-HERE"
                     rend="inline"/>-->
                  reflects the fact that the segmentation of image regions is locally homogeneous.
                  For the domain of character segmentation we propose to use higher order MRFs with
                  cliques covering the stroke properties of the characters.</p>
               <p xml:id="gau.p0021">For a regular lattice <emph>S</emph> the neighbour set
                     <emph>N</emph> of <emph>i</emph> is defined as the set of nearby sites within a
                  radius <emph>r</emph>. A first order MRF involves directly connected pixels in
                  both the horizontal and vertical direction, see <ref target="#figure3">Figure
                     3a</ref>. The numbers <emph>n = 1 ... 5</emph> in the figure indicate the
                  neighbouring sites in an n<hi rend="sup">th</hi> order neighbourhood system. As
                  observed by Roth and Black <ref target="#rothblack2005">(2005</ref>) MRF priors
                  with small neighbourhood systems of only first order limit the expressiveness of
                  the models. Thus <emph>C</emph> is the set of all pixels <emph>s</emph> within a
                  radius <emph>r</emph>, where <emph>r</emph> corresponds to the radius of the mean
                  stroke width. Our experiments for manually segmented characters allocate a mean
                  stroke width of 5 pixels. Thus the prior considers a neighbourhood set of at least
                  third or fourth order. To illustrate the neighbourhood system on our images
                  consider <ref target="#figure3">Figure 3b</ref>. The figure shows one character
                  from our data set with a white circle corresponding to a neighbourhood system of
                  the fourth order.</p>
               <table>
                  <row>
                     <cell>
                        <figure xml:id="figure3">
                           <figDesc>Figure 3a: Neighbourhood System in MRFs</figDesc>
                           <graphic url="support/Fig3a.png"/>
                        </figure>
                     </cell>

                     <cell>
                        <figure>
                           <figDesc>Figure 3b: Glagolitic Character</figDesc>
                           <graphic url="support/Fig3b.png"/>
                        </figure>
                     </cell>
                  </row>
               </table>

               <p xml:id="gau.p0022">From the information of the multi-spectral image the
                  observation model <hi rend="italic">&#x03a8;<hi rend="sub">i</hi>(x<hi rend="sub"
                        >i</hi>)</hi> is extracted. The observation model or image process follows a
                  normal distribution <hi rend="italic">N(μ,Σ)</hi> (Kato, Pong 2006). Each class
                  (foreground/text and background) is represented by its mean vector <hi
                     rend="italic">μ</hi> and covariance matrix <hi rend="italic">Σ</hi>. The
                  entities are modelled by a Gaussian mixture model.</p>
               <p xml:id="gau.p0023">Energy minimisation in finding optimal solutions can be done
                  either by local methods, like ICM, or global methods like simulated annealing (Li
                  2009). We used ICM to solve this energy which is a good trade-off between quality
                  and computing time (Kato 2006). ICM uses a deterministic strategy to find local
                  minima. It starts with estimation and then selects a label for each pixel that
                  gives the largest decrease of the energy function. The process is repeated until
                  convergence.</p>
            </div>
            <div>
               <head xml:id="section3.3"> Experiments and Results</head>
               <p xml:id="gau.p0024">Our segmentation method has been tested on a varied set of
                  ancient documents. The test set consists of four folia for which ground truth data
                  was generated manually by specialists of our philological team. An example can be
                  seen in <ref target="#figure4">Figure 4a</ref> showing a single line from folio 29
                  recto from a single band with high contrast (BP 450). As stated in <ref
                     target="#section2">"Multispectral Image Acquisition," above,</ref> our MSI
                  acquired nine spectral images with a spatial resolution of 565 dpi. The proposed
                  MRF based binarisation approach is compared to state-of-the-art algorithms
                  developed especially for historical, low contrast or noisy document images. The
                  first method is an adaptation of the <emph>k-</emph>means algorithm proposed by
                  Leydier et al. (<ref target="#leydierbourgeoisemptoz2004">2004</ref>), but in
                  contrast to the original work we use the MSI data instead of a colour image as
                  input, resulting in a nine dimensional feature space. Furthermore, we compare the
                  MRF based approach to the Sauvola binarisation method (<ref
                     target="#sauvolapietikainen2000">Sauvola, et al. 2000</ref>). Since
                  thresholding algorithms perform on single gray level images, the method of Sauvola
                  and Pietikannen (2006) is performed on a single band image with the best contrast
                  (BP 450). </p>
               <p xml:id="gau.p0025">To evaluate the results and to rank the performance of the
                  different methods, we use the statistical measures of <term>precision</term> and
                     <term>recall</term> (<ref target="#gatosntirogiannispratikakis2009">Gatos,
                     Ntirogiannis, et al. 2009</ref>): <graphic url="support/TP.png" height="150px"
                  /> where <emph>TP</emph> is the number of true positives, <emph>FP</emph> the
                  number of false positives, and <emph>FN</emph> the number of false negatives. A
                  pixel is classified as true positive if it is identified correctly. It is
                  classified as false positive if it is wrongly classified as a match, i.e., pixels
                  which are detected as text, although they belong to the background. Finally, false
                  negative describes a foreground pixel that was wrongly classified as belonging to
                  the background.</p>
               <p xml:id="gau.p0026">The first experiment aimed at analysing the behaviour of the
                  neighbourhood system N and the weighting parameter <hi rend="italic">β</hi>. <ref
                     target="#Table2">Table 2</ref> shows the precision and recall rate for <hi
                     rend="italic">β = 0.1</hi> and <hi rend="italic">β = 0.3</hi> and a
                  neighbourhood system n = 1…5. It can be seen that the recall values are very low
                  for n &lt; 3 which results from the background noise, i.e., noise is detected as
                  text when the neighbourhood considered is too small. The best solution is obtained
                  with n = 4 and <hi rend="italic">β = 0.1</hi> which is in concordance to the
                  proposed stroke characteristics.</p>
               <table rend="boxed" xml:id="Table2">
                  <head>Evaluation of Order and <hi rend="italic">β</hi></head>
                  <row>
                     <cell/>
                     <cell>n = 1</cell>
                     <cell>n = 2</cell>
                     <cell>n = 3</cell>
                     <cell>n = 4</cell>
                     <cell>n = 5</cell>
                  </row>
                  <row>
                     <cell>precision</cell>
                     <cell>0.81</cell>
                     <cell>0.81</cell>
                     <cell>0.82</cell>
                     <cell>0.82</cell>
                     <cell>0.80</cell>
                  </row>
                  <row>
                     <cell>recall</cell>
                     <cell>0.62</cell>
                     <cell>0.65</cell>
                     <cell>0.65</cell>
                     <cell>0.78</cell>
                     <cell>0.70</cell>
                  </row>
                  <row>
                     <cell/>
                     <cell>n = 1</cell>
                     <cell>n = 2</cell>
                     <cell>n = 3</cell>
                     <cell>n = 4</cell>
                     <cell>n = 5</cell>
                  </row>
                  <row>
                     <cell>precision</cell>
                     <cell>0.80</cell>
                     <cell>0.79</cell>
                     <cell>0.83</cell>
                     <cell>0.79</cell>
                     <cell>0.75</cell>
                  </row>
                  <row>
                     <cell>recall</cell>
                     <cell>0.67</cell>
                     <cell>0.73</cell>
                     <cell>0.66</cell>
                     <cell>0.80</cell>
                     <cell>0.66</cell>
                  </row>
               </table>
               <p xml:id="gau.p0027">Generally it can be said that the smaller the considered
                  neighbourhood system, the more noise emerges in the background. On the other side,
                  a neighbourhood set considering too many pixels leads to missing characters or to
                  closed character gaps or holes. The same can be said for the influence of <hi
                     rend="italic">β</hi>. </p>
               <p xml:id="gau.p0028">The precision and recall rate for the ground truth data of the
                  four manually segmented folia can be seen in <ref target="#Table3">Table
                  3</ref>.</p>
               <table rend="boxed" xml:id="Table3">
                  <head>Precision and Recall Rate</head>
                  <row>
                     <cell>
                        <hi>Folio</hi>
                     </cell>
                     <cell>
                        <hi> </hi>
                     </cell>
                     <cell>
                        <hi>k-</hi>
                        <hi>means</hi>
                     </cell>
                     <cell>
                        <hi>MRF</hi>
                     </cell>
                     <cell>
                        <hi>Sauvola</hi>
                     </cell>
                  </row>
                  <row>
                     <cell>17 recto</cell>
                     <cell>precision</cell>
                     <cell>0,58</cell>
                     <cell>0,93</cell>
                     <cell>0,67</cell>
                  </row>
                  <row>
                     <cell> </cell>
                     <cell>recall</cell>
                     <cell>0,34</cell>
                     <cell>0,64</cell>
                     <cell>0,72</cell>
                  </row>
                  <row>
                     <cell>29 recto</cell>
                     <cell>precision</cell>
                     <cell>0,67</cell>
                     <cell>0,82</cell>
                     <cell>0,63</cell>
                  </row>
                  <row>
                     <cell> </cell>
                     <cell>recall</cell>
                     <cell>0,72</cell>
                     <cell>0,78</cell>
                     <cell>0,61</cell>
                  </row>
                  <row>
                     <cell>30 verso</cell>
                     <cell>precision</cell>
                     <cell>0,54</cell>
                     <cell>0,90</cell>
                     <cell>0,73</cell>
                  </row>
                  <row>
                     <cell> </cell>
                     <cell>recall</cell>
                     <cell>0,75</cell>
                     <cell>0,68</cell>
                     <cell>0,72</cell>
                  </row>
                  <row>
                     <cell>27 recto</cell>
                     <cell>precision</cell>
                     <cell>0,85</cell>
                     <cell>0,92</cell>
                     <cell>0,55</cell>
                  </row>
                  <row>
                     <cell> </cell>
                     <cell>recall</cell>
                     <cell>0,69</cell>
                     <cell>0,81</cell>
                     <cell>0,64</cell>
                  </row>
                  <row>
                     <cell>Average</cell>
                     <cell>precision</cell>
                     <cell>0,66</cell>
                     <cell>0,89</cell>
                     <cell>0,65</cell>
                  </row>
                  <row>
                     <cell> </cell>
                     <cell>recall </cell>
                     <cell>0,63</cell>
                     <cell>0,73</cell>
                     <cell>0,67</cell>
                  </row>
               </table>
               <p xml:id="gau.p0029">Especially for folio 17 recto and 30 verso the folia segmented
                  with the <emph>k-</emph>means algorithm show only suboptimal results due to low
                  contrast. The thresholding method shows a better recall rate of average 0.67, but
                  has lower precision (0.65). The proposed MRF method has the best performance with
                  an average precision rate of 0.89 and an average recall rate of 0.73. A
                  description of the results is given for folio 29 recto. <ref target="#figure4"
                     >Figure 4</ref> shows the results from folio 29 recto after the segmentation
                  with the Sauvola binarisation method (<emph>4b</emph>), <emph>k-</emph>means
                  clustering (<emph>4c</emph>), and the MRF approach (<emph>4d</emph>) with
                  parameters <hi rend="italic">β = 0.1</hi> and a neighbourhood of fourth order.</p>
               <figure xml:id="figure4">
                  <figDesc>Figure 4a: 29r Original</figDesc>
                  <graphic url="support/Fig4a.png"/>
               </figure>
               <figure>
                  <figDesc>Figure 4b: Sauvola</figDesc>
                  <graphic url="support/Fig4b.png"/>
               </figure>
               <figure>
                  <figDesc>Figure 4c: <emph>k</emph>-means</figDesc>
                  <graphic url="support/Fig4c.png"/>
               </figure>
               <figure>
                  <figDesc>Figure 4d: MRF</figDesc>
                  <graphic url="support/Fig4d.png"/>
               </figure>

               <!--
               <p>
                  <figure>
                     <graphic url="./ObjectReplacements/Object 35"/>
                  </figure>
               </p>
               <p/>
               <p>
                  <figure>
                     <graphic url="./ObjectReplacements/Object 36"/>
                  </figure>
               </p>
               <p>
                  <emph/>
               </p>
               <p>
                  <figure>
                     <graphic url="./ObjectReplacements/Object 37"/>
                  </figure>
               </p>
               <p/>
               -->
               <p xml:id="gau.p0030">It can be seen that especially the thresholding image contains
                  noise in the background and even within the characters. The resulting binary image
                  from the <emph>k-</emph>means method fails to identify the rightmost character,
                  and others are broken. The result of the MRF approach segments even the rightmost
                  character which has very low contrast. Moreover, the characters do not show
                  missing or broken parts like the results from the <emph>k-</emph>means algorithm.
                  Conspicuously, the recall rate is sometimes very high; for example, in folio 30
                  verso, when segmented with k-means. But it can be seen that the precision is very
                  low at the same time, which denotes that the letters are detected rather as blobs
                  than as characters. Thus the segmented characters cannot be identified any
                  more.</p>
            </div>
         </div>
         <div>
            <head xml:id="section4">Further Project Applications</head>
            <p xml:id="gau.p0031">A robust binarisation algorithm forms the basis for a number of
               further analyses. In an interdisciplinary approach we built a toolbox for manuscript
               analysis that combines several computer applications supporting traditional
               codicological and palaeographic investigations. Some of them shall be presented in
               the following.</p>
            <div>
               <head xml:id="section4.1">Character Decomposition and Primitive Extraction</head>
               <p xml:id="gau.p0032">After the binarisation described in <ref target="#section3"
                     >"Foreground-Background Separation," above</ref>, each character is reduced to
                  a skeleton that serves as the basis for primitive extraction. The quality of the
                  binary image is essential for the stroke extraction procedure and the number of
                  true positives grows in correlation with the readability of the binary images.</p>
               <p xml:id="gau.p0033">In our approach we adapted a linguistic method of graphetic
                  script description developed by Miklas <ref target="#miklas1992unpublished">(1992
                     unpublished</ref>), which is based mainly on binary principles. He
                  distinguishes two categories of character features: a) <term>dynamic</term>,
                  pertaining to the realisation (production) of the letter, and b)
                     <term>static</term>, describing the shape of the character, i.e., which
                  characteristic elements, or <term>primitives</term>, does it consist of
                  (perception). Sample static character features are:</p>
               <table rend="boxed" xml:id="Table4">
                  <head>Static Character Features (<ref target="#villsablatnig2008">Vill, Sablatnig
                        2008</ref>)</head>
                  <row>
                     <cell>
                        <hi>Number</hi>
                     </cell>
                     <cell>
                        <hi>Feature Name</hi>
                     </cell>
                  </row>
                  <row>
                     <cell>Feature 1</cell>
                     <cell>Number of static strokes</cell>
                  </row>
                  <row>
                     <cell>Feature 2</cell>
                     <cell>Number of nodes</cell>
                  </row>
                  <row>
                     <cell>Feature 3</cell>
                     <cell>Number of straight static strokes</cell>
                  </row>
                  <row>
                     <cell>Feature 4</cell>
                     <cell>Number of bent static strokes</cell>
                  </row>
                  <row>
                     <cell>Feature 5</cell>
                     <cell>Number of vertical static strokes</cell>
                  </row>
                  <row>
                     <cell>Feature 6</cell>
                     <cell>Number of horizontal static strokes</cell>
                  </row>
                  <row>
                     <cell>Feature 7</cell>
                     <cell>Number of loops</cell>
                  </row>
                  <row>
                     <cell>Feature 8</cell>
                     <cell>Number of open ends</cell>
                  </row>
                  <row>
                     <cell>Feature 9</cell>
                     <cell>Number of closed elements</cell>
                  </row>
               </table>
               <p xml:id="gau.p0034">Based on its skeleton each character-form is dissected into
                     <term>nodes</term> and <term>strokes</term>. <term>Nodes</term> are defined as
                  junctions in the skeleton with a minimum of three strokes crossing, while
                     <term>strokes</term> are skeleton segments between nodes, from a node to an
                  endpoint in the character (see <ref target="#figure5">Figure 5</ref>), or loops
                     (<ref target="#villsablatnig2008">Vill, Sablatnig 2008</ref>).</p>
               
                  <figure xml:id="figure5">
                     <figDesc>Figure 5: Schematic Views of Static Stroke Segmentation of Glagolitic
                        Character</figDesc>
                     <graphic url="support/Fig5.png"/>
                  </figure>
               
               <p xml:id="gau.p0035">The individual characteristics of each stroke (vertical,
                  horizontal, straight, bent, etc.) constitute a sensitive classification system
                     (<ref target="#villsablatnig2008">Vill, Sablatnig 2008</ref>) that can even
                  cover differences between individual hands.</p>
               <p xml:id="gau.p0036">A precision and recall evaluation was executed on image data
                  from the manuscripts, as well as on samples from a professional calligrapher (<ref
                     target="#Table5">Table 5</ref>). Both datasets were also evaluated as ground
                  truth data by our philological team. The average precision TP rate coincides
                  closely with the ground truth data. The recall rate indicated good results with
                  0.20 FN for the <title level="m">Missale Sinaiticum</title> and 0.17 for the
                  calligrapher’s data set. </p>
               <!--
               <p>
                  <emph>Table 5: Results of </emph>
                  <emph>Static Character Feature</emph>
                  <emph>Calculation</emph>
               </p>
               -->

               <table xml:id="Table5">
                  <head>Static Character Feature Calculation</head>
                  <row>
                     <cell>
                        <figure>
                           <graphic url="support/table5.png" height="250px"/>
                        </figure></cell>
                  </row>
               </table>


               <p xml:id="gau.p0037">These results proved that the adaptation of philological
                  criteria for computer application is feasible for the evaluation of static
                  graphetic features (for further details see <ref target="#villsablatnig2008">Vill,
                     Sablatnig 2008</ref>).</p>
            </div>
            <div xml:id="section4.2">
               <head>Character Database</head>
               <p xml:id="gau.p0038">After the automatic decomposition of static strokes, the
                  calculated data can be transferred to a database (<ref
                     target="#gauvillkleberdiemmiklassablatnig2010">Gau, Vill, et al. 2010</ref>)
                  with fundamental overview, query, statistics, and print out options (<ref
                     target="#figure6">Figure 6</ref>, left side).</p>
               
                  <figure xml:id="figure6">
                     <figDesc>Figure 6: Graphical User Interface of the Character Database</figDesc>
                     <graphic url="support/Fig6.png"/>
                  </figure>
               

               <p xml:id="gau.p0039">The graphical user interface of the database also permits
                  manual evaluation according to the same criteria as the automatic evaluation (<ref
                     target="#figure6">Figure 6</ref>, right side). This comparison between computer
                  and human perception provides ground truth for the quality of the computer's
                  primitive extraction on the one hand and for psycholinguistics on the other.</p>
            </div>
            <div>
               <head xml:id="section4.3">Layout Analysis</head>
               <p xml:id="gau.p0040">In a subsequent application we perform an analysis of the page
                  layout (ruling, margins, decorations, etc.) based on the binary images provided by
                  the separation step. The ruling (line) structure is automatically detected by the
                  script flow and then extrapolated on those parts of damaged pages, where the
                  script is not visible, by using <foreign xml:lang="gr">a priori</foreign>
                  knowledge of the document layout scheme (for details see Kleber, Sablatnig, et al.
                  2008).</p>
               
                  <figure xml:id="figure7">
                     <figDesc>Figure 7: a) Results of Semi-Automatic Layout Analysis and b)
                        Underlying Layout Scheme (A Priori Knowledge)</figDesc>
                     <graphic url="support/Fig7.jpg"/>
                  </figure>
               
               <p xml:id="gau.p0041">
                  <ref target="#figure7">Figure 7a</ref> illustrates a sample result of the
                  semi-automatic layout analysis with red lines calculated from detected script and
                  green and blue lines extrapolated according to the <foreign xml:lang="gr">a
                     priori</foreign> knowledge (<ref target="#figure7">Figure 7b</ref>) of the
                  layout scheme.</p>
               <p xml:id="gau.p0042">This combination of IT with philological expertise made it
                  possible to automate layout analysis even for damaged manuscripts to such an
                  extent that it can automatically discern textual areas from margins and script
                  from decorations or other high-contrast non-textual elements, like patches of
                  mould.</p>
            </div>
         </div>
         <div xml:id="section5">
            <head>Discussion and Conclusion</head>
            <p xml:id="gau.p0043">In this paper it has been shown that the examination of corrupted
               manuscripts can be widely enhanced by MSI. Foreground-background separation based on
               spectral and spatial stroke features serves as input data for a number of consecutive
               investigations like character decomposition and layout analysis. The quality of the
               binary images is of crucial importance for these subsequent procedures. In the
               future, a more detailed evaluation of the foreground-background separation will
               include a larger variety of folia and the generation of ground truth data from
               several experts, in order to avoid subjectivity. Apart from the above described
               binarisation, in our project we also used MSI for the combination of spectral bands
               by principal component analysis, which increased the readability considerably. Some
               resulting spectral components highlight codicological details like the ruling, and
               the text- and decoration-inks.</p>
            <p xml:id="gau.p0044">While computational script analysis methods have long been used in
               other disciplines like graphology, forensics, or pedagogy, they have been introduced
               only recently into the philological (historical) research areas of palaeography on
               the one hand, and graphetics and graphemics on the other. By combining philological
               and technical expertise we created a quantifiable method to classify (in our case:
               Glagolitic) characters, thereby also preparing the ground for optical character
               recognition of hand-written (especially damaged) documents. In the future we will
               expand the number of test samples and ground truth data from different experts, on
               the one hand, and test and expand the automatable catalogue of character features for
               its application to all alphabetic writing systems, on the other.</p>
            <p xml:id="gau.p0045">With the evaluation of character features deriving from the
               automatic character decomposition we can for the first time apply modern database
               query routines also to traditional palaeographical questions and closely compare even
               very similar hands. This will further empirical answers to questions of cultural
               history, for example, about the provenance of early Glagolitic manuscripts.</p>
            <p xml:id="gau.p0046">While the semi-automatic layout analysis still depends on <foreign
                  xml:lang="gr">a priori</foreign> knowledge of the layout, it is useful for heavily
               degraded manuscripts, where the procedure supplies additional information beyond the
               mere layout scheme. Thus we can estimate, for example, the amount of missing text for
               the text reconstruction, detect palimpsest lines and identify missing page fragments
                  (<ref target="#klebersablatnig2010">Kleber, Sablatnig 2010</ref>).</p>
            <p xml:id="gau.p0047">As the routines for layout analysis, primitive extraction, and
               character decomposition have proven helpful for philological examination, they were
               integrated into a <title level="m">Toolbox for Manuscript Analysis</title> (<ref
                  target="#gauvillkleberdiemmiklassablatnig2010">Gau, Vill, et al. 2010</ref>) with
               a graphical user interface for document and script analysis of manuscripts. For
               better usability the toolbox is currently being converted into a Java based
               environment.</p>
         </div>
      </body>
      <back>
         <div>
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