Diffuse Optical Tomography is a diagnostic imaging modality where optical parameters such as absorption coefficient, scattering coefficient and refractive index distributions are recovered to form the internal tissue metabolic image. Near-infrared (NIR) light has the potential to be used as a noninvasive means of diagnostic imaging within the human breast. Due to the diffusive nature of light in tissue, computational model-based methods are required for functional imaging. The main goal is to recover the spatial variation of optical properties which shed light on the different metabolic states of tissue and tissue like media. This thesis addresses the issue of quantitative recovery of optical properties of tissue-mimicking phantom and pork tissue using diffuse optical tomography (DOT). The main contribution of the present work is the development of robust, efficient and fast optical property reconstruction algorithms for a direct 3-D DOT imaging system. There are both theoretical and experimental contributions towards the development of an imaging system and procedures to minimize accurate data collection time, overall system automation as well as development of computational algorithms. In nurturing the idea of imaging using NIR light into a fully developed direct 3-D imaging system, challenges from the theoretical and computational aspects have to be met. The recovery of the optical property distribution in the interior of the object from the often noisy boundary measurements on light, is an ill-posed ( and nonlinear) problem. This is particularly true, when one is interested in a direct 3-D image reconstruction instead of the often employed stacking of 2-D cross-sections obtained from solving a set of 2-D DOT problems. In order to render the DOT, a useful diagnostic imaging tool and a robust reconstruction procedure giving accurate and reliable parameter recovery in the scenario, where the number of unknowns far outnumbers the number of independent data sets that can be gathered (for example, the direct 3-D recovery mentioned earlier) is essential. Here, the inversion problem is often solved through iterative methods based on nonlinear optimization for the minimization of a data-model misfit function. An interesting development in this direction has been the development of Broyden’ s and adjoint Broyden’ s methods that avoids direct Jacobian computation in each iteration thereby making the full 3-D a reality. Conventional model based iterative image reconstruction (MoBIIR) algorithm uses Newton’ s and it’s variant methods, where it required repeated evaluation of whole Jacobian, which consumes bulk time in reconstruction process. The explicit secant and adjoint information based fast 2-D/3-D image reconstruction algorithms without repeated evaluation of the Jacobian is proposed in diffuse optical tomography, where the computational time has been decreased many folds by updating the Jacobian successively through low rank update. An alternative route to the iterative solution is attempted by introducing an artificial dynamics in the system and treating the steady-state response of the artificially evolving dynamical system as a solution. The objective is to consider a novel family of pseudo-dynamical 2-D and 3-D systems whose numerical integration in time provides an asymptotic solution to the inverse problem at hand. We convert Gauss-Newton’ s equation for updates into a pseudo-dynamical (PD) form by explicitly adding a time derivative term. As the pseudo-time integration schemes do not need such explicit matrix inversion and depending on the pseudo-time step size, provides for a layer of regularization that in turn helps in superior quality of 2-D and 3-D image reconstruction. A cost effective frequency domain Matlab based 2-D/3-D automated imaging system is designed and built. The complete instrumentation (including PC-based control software) has been developed using a single modulated laser source (wavelength 830nm) and a photo-multiplier tube (PMT). The source and detector fiber change their positions dynamically allowing us to gather data at multiple source and detector locations. The fiber positions are adjusted on the phantom surface automatically for scanning variable size phantoms. A heterodyning scheme was used for reading out the measurement using a lock-in-amplifier. The Matlab program carries out sequence of actions such as instrument control, data acquisition, data organization, data calibration and reconstruction of image. The Gauss-Newton’ s, Broyden’ s, adjoint Broyden’ s and pseudo-time integration algorithms are evaluated using the simulation data as well as data from the experimental DOT system. Validation of the system and the reconstruction algorithms were carried out on a real tissue, a pork tissue with an embedded fat inhomogeneity. The results were found to match the known parameters closely.

A hiperplasia do processo coronóide é uma afecção que causa uma limitada mobilidade mandibular e conseqüente limitação de abertura da boca. Não apresenta sintomatologia dolorosa, e tem progressão lenta, levando o paciente a procurar por tratamento somente se a limitação de abertura for severa a ponto de prejudicar as funções mastigatórias normais. Muitos casos levam clínicos a tratarem o paciente como portador de disfunção da articulação têmporo mandibular (DTM). Este trabalho se propõe a avaliar a tomografia computadorizada (TC) como método para auxiliar na elaboração do diagnóstico e no planejamento cirúrgico desta anomalia, estudando a presença da hiperplasia do processo coronóide pela observação de imagens obtidas por meio da Tomografia Computadorizada Helicoidal, considerando as imagens volumétricas multiplanar e 3D, e as suas associações. Foram utilizadas imagens de arquivo dos exames de tomografia computadorizada helicoidal de 152 pacientes que apresentavam sinais e sintomas de Disfunção Têmporo Mandibular (DTM) encaminhados para a Unidade de Diagnóstico Dento-Maxilo-Facial da Clínica Félix Boada, na cidade de Caracas - Venezuela, para exame tomográfico da ATM. Dos 152 pacientes, foram selecionados 20 casos, que eram de portadores de sinais e/ou sintomas de Disfunção Têmporo Mandibular, mas que, ao exame realizado, constatou-se a presença da hiperplasia do processo coronóide. Os dados dos 20 pacientes foram comparados, de maneira a identificar as possíveis diferenças entre as opiniões de 5 cirurgiões dentistas radiologistas e de 5 cirurgiões dentistas buco-maxilo-faciais. Utilizou-se a técnica da Análise de Médias (Analysis of Means - ANOM), que calcula uma média geral entre os 5 observadores de cada especialidade, e um intervalo que indica quais observadores tiveram opiniões semelhantes e quais tiveram opiniões diversas. Depois foi feita a comparação entre os dois grupos, utilizando o teste das proporções. Em conclusão, os observadores acharam as imagens MPR mais esclarecedoras que as reconstruções volumétricas 3D, na maioria dos casos de hiperplasia do processo coronóide, quando esses recursos foram avaliados separadamente. Contudo, acharam imprescindível a utilização de ambas as imagens, em associação ou não, indicando-as para o estudo da hiperplasia do processo coronóide. A hipomobilidade foi observada na articulação temporomandibular, no lado acometido pela hiperplasia do processo coronóide, em 55,2% dos casos / The Coronoid Process Hyperplasia is an affection that causes a limited mandibular mobility and a consequent limitation in mouth opening. It doesn’t present any painful symptomatology and has a slow progression, leading the patient to look for treatment only when the opening limitation is severe to the point of impairing regular masticatory functions. Many cases lead clinicians to treat the patient as he had a temporomandibular dysfunction. This work proposed an evaluation of the CT as an auxiliary method in the elaboration of the diagnosis and in the surgical planning of that anomaly by studying the presence of the Coronoid Process Hyperplasia through the observation of images obtained by means of the Helicoidal Computerized Tomography, considering the volumetric multiplane and 3D images and their associations. Filed images of Helicoidal Computerized Tomography were used, belonging to the examination of 152 patients who presented symptoms of temporomandibular dysfunction and were all directed to the Dento-Maxillo-Facial Diagnosis Unit of the Clinica Felix Boada in the city of Caracas – Venezuela for TMA tomographic examination. Of the 152 patients 20 were selected who showed signs or symptoms of TMA dysfunction and Coronoid Process Hyperplasia was detected. Data of the 20 patients were compared in order to identify possible differences among the opinions of 5 radiologist specialists and 5 buco-maxillo -facial specialists. The Analysis of Means – ANOM was used to calculate a general average among the 5 specialists in each specialty and a gap that opinions and which ones had different opinions. Afterwards the comparison between the 2 groups was made using the Proportion Test. The observers concluded that the MPR images were more clarifying than the 3D images in most of the cases of coronoid process hyperplasia, especially when those resources were evaluated separately. Although they found vital the utilization of both images in association or not and indicated them to the study of the Coronoid Process Hyperplasia. Hypo mobility was observed in the TMA in the affected side in 55,2% of the cases

A hiperplasia do processo coronóide é uma afecção que causa uma limitada mobilidade mandibular e conseqüente limitação de abertura da boca. Não apresenta sintomatologia dolorosa, e tem progressão lenta, levando o paciente a procurar por tratamento somente se a limitação de abertura for severa a ponto de prejudicar as funções mastigatórias normais. Muitos casos levam clínicos a tratarem o paciente como portador de disfunção da articulação têmporo mandibular (DTM). Este trabalho se propõe a avaliar a tomografia computadorizada (TC) como método para auxiliar na elaboração do diagnóstico e no planejamento cirúrgico desta anomalia, estudando a presença da hiperplasia do processo coronóide pela observação de imagens obtidas por meio da Tomografia Computadorizada Helicoidal, considerando as imagens volumétricas multiplanar e 3D, e as suas associações. Foram utilizadas imagens de arquivo dos exames de tomografia computadorizada helicoidal de 152 pacientes que apresentavam sinais e sintomas de Disfunção Têmporo Mandibular (DTM) encaminhados para a Unidade de Diagnóstico Dento-Maxilo-Facial da Clínica Félix Boada, na cidade de Caracas - Venezuela, para exame tomográfico da ATM. Dos 152 pacientes, foram selecionados 20 casos, que eram de portadores de sinais e/ou sintomas de Disfunção Têmporo Mandibular, mas que, ao exame realizado, constatou-se a presença da hiperplasia do processo coronóide. Os dados dos 20 pacientes foram comparados, de maneira a identificar as possíveis diferenças entre as opiniões de 5 cirurgiões dentistas radiologistas e de 5 cirurgiões dentistas buco-maxilo-faciais. Utilizou-se a técnica da Análise de Médias (Analysis of Means - ANOM), que calcula uma média geral entre os 5 observadores de cada especialidade, e um intervalo que indica quais observadores tiveram opiniões semelhantes e quais tiveram opiniões diversas. Depois foi feita a comparação entre os dois grupos, utilizando o teste das proporções. Em conclusão, os observadores acharam as imagens MPR mais esclarecedoras que as reconstruções volumétricas 3D, na maioria dos casos de hiperplasia do processo coronóide, quando esses recursos foram avaliados separadamente. Contudo, acharam imprescindível a utilização de ambas as imagens, em associação ou não, indicando-as para o estudo da hiperplasia do processo coronóide. A hipomobilidade foi observada na articulação temporomandibular, no lado acometido pela hiperplasia do processo coronóide, em 55,2% dos casos / The Coronoid Process Hyperplasia is an affection that causes a limited mandibular mobility and a consequent limitation in mouth opening. It doesn’t present any painful symptomatology and has a slow progression, leading the patient to look for treatment only when the opening limitation is severe to the point of impairing regular masticatory functions. Many cases lead clinicians to treat the patient as he had a temporomandibular dysfunction. This work proposed an evaluation of the CT as an auxiliary method in the elaboration of the diagnosis and in the surgical planning of that anomaly by studying the presence of the Coronoid Process Hyperplasia through the observation of images obtained by means of the Helicoidal Computerized Tomography, considering the volumetric multiplane and 3D images and their associations. Filed images of Helicoidal Computerized Tomography were used, belonging to the examination of 152 patients who presented symptoms of temporomandibular dysfunction and were all directed to the Dento-Maxillo-Facial Diagnosis Unit of the Clinica Felix Boada in the city of Caracas – Venezuela for TMA tomographic examination. Of the 152 patients 20 were selected who showed signs or symptoms of TMA dysfunction and Coronoid Process Hyperplasia was detected. Data of the 20 patients were compared in order to identify possible differences among the opinions of 5 radiologist specialists and 5 buco-maxillo -facial specialists. The Analysis of Means – ANOM was used to calculate a general average among the 5 specialists in each specialty and a gap that opinions and which ones had different opinions. Afterwards the comparison between the 2 groups was made using the Proportion Test. The observers concluded that the MPR images were more clarifying than the 3D images in most of the cases of coronoid process hyperplasia, especially when those resources were evaluated separately. Although they found vital the utilization of both images in association or not and indicated them to the study of the Coronoid Process Hyperplasia. Hypo mobility was observed in the TMA in the affected side in 55,2% of the cases

Wood is a limited natural resource whose characteristics have been difficult to identify by advanced technology. The most expensive is a hardwood. There is a desire to optimize the production of wood products by minimizing waste and maximizing output. It could be achieved if one had capabilities to evaluate the common wood structures ― knots, rots, empty spaces and other defects. There are many nondestructive testing methods that could be applied to the evaluation of the inner quality of a log. The most successful one is an x-ray computerized tomography. This thesis covers principles of computerized tomography and image reconstruction algorithms. Testing was performed on implementations of tomographic image reconstruction algorithms using synthetic and real data. Research on an application of an x-ray computerized tomography for the analysis of wood structures was made. Inspection of glued zones in glued wooden articles was accomplished using tomographic imaging. Guidelines for the creation of a wood specialized x-ray computerized tomograph were given.

Made available in DSpace on 2016-06-02T19:58:04Z (GMT). No. of bitstreams: 1 3535.pdf: 15531173 bytes, checksum: 0bec1dee483a9cf070857af8977686a0 (MD5) Previous issue date: 2011-03-18 / Financiadora de Estudos e Projetos / Arborization is fundamental in urban spaces, due to the significant benefits it provides. To important issue to guarantee the adequacy of the role it plays is its maintenance. To this purpose, an application of preventive methods of diagnosis is recommended, allowing the evaluation of external and internal conditions of tress. Currently, the analysis of urban trees is subjectivity. For a complete and secure analysis, it is important to associate this visual external analysis to an internal analysis. This could be done by applying non-destructive techniques, wich allows an internal visualization of the tree through a tomographic image, without causing it any damage. Among the non-destructive techniques, that have applicability in the internal evaluation of urban trees, the technique of stress waves can be highlighted. Considering the great benefits that this technique can provide in the evaluation of urban trees, this research seeks to verify its scientific and technique viability, analyzing its reliability and also establishing some parameters of application. Studies with 12 trees of the Caesalpinea peltophoroides species (popularly known as Sibipiruna) have been carried out. The stress waves equipment was applied to sections of 50, 90 and 130 cm from the trees basis, generating tomographic images of these sections. Afterwards, the trees were cut at the level of these sections and, in order to compare these images, some pictures of them were made. The results show that the trees waves technique presents large applicability for internal evaluation of urban trees, achieving significant results. Also some parameters for the application of this technique were established. For instance, it is necessary to determinate the speed reference of waves propagation for the interpretation of tomographic images, as well as it is to determinate the best height of the assays section. The latter consisting on the height of the diameter to the chest height (DAP), where average density of the tree is representative. / A arborização é fundamental nos espaços urbanos, devido aos importantes benefícios que proporciona. Para garantir que esta exerça adequadamente seu papel, é importante a sua manutenção, na qual é necessário o emprego de métodos de diagnóstico preventivos, que permitam avaliar as condições externas e internas das árvores. Atualmente, a análise de árvores urbanas é realizada basicamente pela análise visual externa, a qual apresenta grande subjetividade. Para uma análise completa e segura é importante que a análise visual externa seja acompanhada de uma análise interna. Esta pode ser realizada por meio de técnicas nãodestrutivas, que possibilitam a visualização interna da árvore através da imagem tomográfica, sem causar nenhum dano a esta. Dentre as técnicas não-destrutivas existentes, com aplicabilidade na avaliação interna de árvores urbanas, pode-se destacar a técnica de ondas de tensão. Diante dos grandes benefícios que esta técnica pode proporcionar na avaliação de árvores urbanas, esta pesquisa buscou verificar sua viabilidade técnica e científica, analisando a sua confiabilidade e estabelecendo parâmetros para sua aplicação. Foram realizados estudos com 12 árvores da espécie Caesalpinea peltophoroides (conhecida popularmente como Sibipiruna), nas quais foram realizadas medições em seções a 50, 90 e 130 cm da base, empregando o equipamento de ondas de tensão, o qual gerou as imagens tomográficas das seções. Em seguida, as árvores foram cortadas nas seções de ensaio e fotografadas, para posterior comparação com a imagem tomográfica gerada. Os resultados permitiram verificar que a técnica de ondas de tensão apresenta grande viabilidade de aplicação na avaliação interna de árvores urbanas, com resultados bastante significativos. Foi possível também estabelecer alguns parâmetros de aplicação da técnica, como a necessidade da determinação da velocidade de propagação da onda de referência, para a interpretação da imagem tomográfica e a determinação da melhor altura da seção para realização dos ensaios, a qual consistiu na altura do diâmetro à altura do peito (DAP), na qual se encontra a representatividade da densidade média da árvore.

Biomedical optical imaging is capable of providing functional information of the soft bi-ological tissues, whose applications include imaging large tissues, such breastand brain in-vivo. Biomedical optical imaging uses near infrared light (600nm-900nm) as the probing media, givin ganaddedadvantageofbeingnon-ionizingimagingmodality. The tomographic technologies for imaging large tissues encompasses diffuse optical tomogra-phyandphotoacoustictomography. Traditional image reconstruction methods indiffuse optical tomographyemploysa �2-norm based regularization, which is known to remove high frequency no is either econstructed images and make the mappearsmooth. Hence as parsity based image reconstruction has been deployed for diffuse optical tomography, these sparserecov-ery methods utilize the �p-norm based regularization in the estimation problem with 0≤ p<1. These sparse recovery methods, along with an approximation to utilizethe �0-norm, have been used forther econstruction of diffus eopticaltomographic images.The comparison of these methods was performed by increasing the sparsityinthesolu-tion. Further a model resolution matrix based framework was proposed and shown to in-duceblurinthe�2-norm based regularization framework for diffuse optical tomography. This model-resolution matrix framework was utilized in the optical imaged econvolution framework. A basis pursuitdeconvolution based on Split AugmentedLagrangianShrink-ageAlgorithm(SALSA)algorithm was used along with the Tikhonovregularization step making the image reconstruction into a two-step procedure. This new two-step approach was found to be robust with no iseandwasabletobetterdelineatethestructureswhichwasevaluatedusingnumericalandgelatinphantom experiments. Modern diffuse optical imaging systems are multi-modalin nature, where diffuse optical imaging is combined with traditional imaging modalitiessuc has Magnetic Res-onanceImaging(MRI),or Computed Tomography(CT). Image-guided diffuse optical tomography has the advantage of reducingthetota lnumber of optical parameters beingreconstructedtothenumber of distinct tissue types identified by the traditional imaging modality, converting the optical image-reconstruction problem fromunder-determined innaturetoover-determined. In such cases, the minimum required measurements might be farless compared to those of the traditional diffuse optical imaging. An approach to choose these measurements optimally based on a data-resolution matrix is proposed, and it is shown that it drastically reduces the minimum required measurements (typicalcaseof240to6) without compromising the image reconstruction performance. In the last part of the work , a model-based image reconstruction approaches in pho-toacoustic tomography (which combines light and ultra sound) arestudied as it is know that these methods have a distinct advantage compared to traditionalanalytical methods in limited datacase. These model-based methods deployTikhonovbasedregularizationschemetoreconstruct the initial pressure from the boundary acoustic data. Again a model-resolution for these cases tend to represent the blurinduced by the regularization scheme. A method that utilizes this blurringmodelandper forms the basis pursuit econ-volution to improve the quantitative accuracy of the reconstructed photoacoustic image is proposed and shown to be superior compared to other traditional methods. Moreover, this deconvolution including the building of model-resolution matrixis achievedvia the Lanczosbidiagonalization (least-squares QR) making this approach computationally ef-ficient and deployable inreal-time. Keywords Medical imaging, biomedical optical imaging, diffuse optical tomography, photoacous-tictomography, multi-modalimaging, inverse problems,sparse recovery,computational methods inbiomedical optical imaging.

Diffuse optical tomography uses near infrared (NIR) light as the probing media to recover the distributions of tissue optical properties. It has a potential to become an adjunct imaging modality for breast and brain imaging, that is capable of providing functional information of the tissue under investigation. As NIR light propagation in the tissue is dominated by scattering, the image reconstruction problem (inverse problem) tends to be non-linear and ill-posed, requiring usage of advanced computational methods to compensate this. Traditional image reconstruction methods in diffuse optical tomography employ l2 –norm based regularization, which is known to remove high frequency noises in the re-constructed images and make them appear smooth. The recovered contrast in the reconstructed image in these type of methods are typically dependent on the iterative nature of the method employed, in which the non-linear iterative technique is known to perform better in comparison to linear techniques. The usage of non-linear iterative techniques in the real-time, especially in dynamical imaging, becomes prohibitive due to the computational complexity associated with them. In the rapid dynamic diffuse optical imaging, assumption of a linear dependency in the solutions between successive frames results in a linear inverse problem. This new frame work along with the l1–norm based regularization can provide better robustness to noise and results in a better contrast recovery compared to conventional l2 –based techniques. Moreover, it is shown that the proposed l1-based technique is computationally efficient compared to its counterpart(l2 –based one). The proposed framework requires a reasonably close estimate of the actual solution for the initial frame and any suboptimal estimate leads to erroneous reconstruction results for the subsequent frames. Modern diffuse optical imaging systems are multi-modal in nature, where diffuse optical imaging is combined with traditional imaging modalities such as MRI, CT, and Ultrasound. A novel approach that can more effectively use the structural information provided by the traditional imaging modalities in these scenarios is introduced, which is based on prior image constrained- l1 minimization scheme. This method has been motivated by the recent progress in the sparse image reconstruction techniques. It is shown that the- l1 based frame work is more effective in terms of localizing the tumor region and recovering the optical property values both in numerical and gelatin phantom cases compared to the traditional methods that use structural information.

Diffuse optical tomography uses near infrared (NIR) light as the probing media to re-cover the distributions of tissue optical properties with an ability to provide functional information of the tissue under investigation. As NIR light propagation in the tissue is dominated by scattering, the image reconstruction problem (inverse problem) is non-linear and ill-posed, requiring usage of advanced computational methods to compensate this. Diffuse optical image reconstruction problem is always rank-deficient, where finding the independent measurements among the available measurements becomes challenging problem. Knowing these independent measurements will help in designing better data acquisition set-ups and lowering the costs associated with it. An optimal measurement selection strategy based on incoherence among rows (corresponding to measurements) of the sensitivity (or weight) matrix for the near infrared diffuse optical tomography is proposed. As incoherence among the measurements can be seen as providing maximum independent information into the estimation of optical properties, this provides high level of optimization required for knowing the independency of a particular measurement on its counterparts. The utility of the proposed scheme is demonstrated using simulated and experimental gelatin phantom data set comparing it with the state-of-the-art methods. The traditional image reconstruction methods employ ℓ2-norm in the regularization functional, resulting in smooth solutions, where the sharp image features are absent. The sparse recovery methods utilize the ℓp-norm with p being between 0 and 1 (0 ≤ p1), along with an approximation to utilize the ℓ0-norm, have been deployed for the reconstruction of diffuse optical images. These methods are shown to have better utility in terms of being more quantitative in reconstructing realistic diffuse optical images compared to traditional methods. Utilization of ℓp-norm based regularization makes the objective (cost) function non-convex and the algorithms that implement ℓp-norm minimization utilizes approximations to the original ℓp-norm function. Three methods for implementing the ℓp-norm were con-sidered, namely Iteratively Reweigthed ℓ1-minimization (IRL1), Iteratively Reweigthed Least-Squares (IRLS), and Iteratively Thresholding Method (ITM). These results in-dicated that IRL1 implementation of ℓp-minimization provides optimal performance in terms of shape recovery and quantitative accuracy of the reconstructed diffuse optical tomographic images. Photoacoustic tomography (PAT) is an emerging hybrid imaging modality combining optics with ultrasound imaging. PAT provides structural and functional imaging in diverse application areas, such as breast cancer and brain imaging. A model-based iterative reconstruction schemes are the most-popular for recovering the initial pressure in limited data case, wherein a large linear system of equations needs to be solved. Often, these iterative methods requires regularization parameter estimation, which tends to be a computationally expensive procedure, making the image reconstruction process to be performed off-line. To overcome this limitation, a computationally efficient approach that computes the optimal regularization parameter is developed for PAT. This approach is based on the least squares-QR (LSQR) decomposition, a well-known dimensionality reduction technique for a large system of equations. It is shown that the proposed framework is effective in terms of quantitative and qualitative reconstructions of initial pressure distribution.

The dissertation deals with the image processing in digital holographic microscopy and X-ray computed tomography. The focus of the work lies in the proposal of data processing techniques to meet the needs of the biological experiments. Transmitted light holographic microscopy is particularly used for quantitative phase imaging of transparent microscopic objects such as living cells. The phase images are affected by the phase aberrations that make the analysis particularly difficult. Here, we present a novel algorithm for dynamical processing of living cells phase images in a time-lapse sequence. The algorithm compensates for the deformation of a phase image using weighted least squares surface fitting. Moreover, it identifies and segments the individual cells in the phase image. This property of the algorithm is important for real-time cell quantitative phase imaging and instantaneous control of the course of the experiment. The efficiency of the propounded algorithm is demonstrated on images of rat fibrosarcoma cells using an off-axis holographic microscope. High resolution X-ray computed tomography is increasingly used technique for the study of the small rodent bones micro-structure. In this part of the work, the trabecular and cortical bone morphology is assessed in the distal half of rat femur. We developed new method for mapping the cortical position and dimensions from a central longitudinal axis with one degree angular resolution. This method was used to examine differences between experimental groups. The bone position in tomographic slices is aligned before the mapping using the propound standardization procedure. The activity of remodelling process of the long bone is studied on the system of cortical canals.