Szymon Tamborski

Assessment of the flow velocity of blood cells in a microfluidic device using joint spectral and time domain optical coherence tomography

Although Doppler optical coherence tomography techniques have enabled the imaging of blood flow in mid-sized vessels in biological tissues, the generation of velocity maps of capillary networks remains a challenge. To better understand the origin and information content of the Doppler signal from small vessels and limitations of such measurements, we used joint spectral and time domain optical coherence tomography to monitor the flow in a model, semitransparent microchannel device. The results obtained for Intralipid, whole blood, as well as separated red blood cells indicate that the technique is suitable to record velocity profiles in vitro, in a range of microchannel configurations.

Extended-focus optical coherence microscopy for high-resolution imaging of the murine brain

We propose a new method and optical instrumentation for mouse brain imaging based on extended-focus optical coherence microscopy. This in vivo imaging technique allows the evaluation of the cytoarchitecture at cellular level and the circulation system dynamics in three dimensions. This minimally invasive and non-contact approach is performed without the application of contrasting agents. The optical design achieved a resolution of 2.2 μm over a distance of 800 μm, which was sufficient to obtain a detailed three-dimensional image of a wild-type mouses brain down to the layer III of the cortex. Intrinsically contrasted microvessels and structures similar to the bodies of neurons were distinguishable.

Optical coherence microscopy as a novel, non-invasive method for the 4D live imaging of early mammalian embryos

Imaging of living cells based on traditional fluorescence and confocal laser scanning microscopy has delivered an enormous amount of information critical for understanding biological processes in single cells. However, the requirement for a high numerical aperture and fluorescent markers still limits researchers’ ability to visualize the cellular architecture without causing short- and long-term photodamage. Optical coherence microscopy (OCM) is a promising alternative that circumvents the technical limitations of fluorescence imaging techniques and provides unique access to fundamental aspects of early embryonic development, without the requirement for sample pre-processing or labeling. In the present paper, we utilized the internal motion of cytoplasm, as well as custom scanning and signal processing protocols, to effectively reduce the speckle noise typical for standard OCM and enable high-resolution intracellular time-lapse imaging. To test our imaging system we used mouse and pig oocytes and embryos and visualized them through fertilization and the first embryonic division, as well as at selected stages of oogenesis and preimplantation development. Because all morphological and morphokinetic properties recorded by OCM are believed to be biomarkers of oocyte/embryo quality, OCM may represent a new chapter in imaging-based preimplantation embryo diagnostics.

Spectrometer calibration for spectroscopic Fourier domain optical coherence tomography

We propose a simple and robust procedure for Fourier domain optical coherence tomography (FdOCT) that allows to linearize the detected FdOCT spectra to wavenumber domain and, at the same time, to determine the wavelength of light for each point of detected spectrum. We show that in this approach it is possible to use any measurable physical quantity that has linear dependency on wavenumber and can be extracted from spectral fringes. The actual values of the measured quantity have no importance for the algorithm and do not need to be known at any stage of the procedure. As example we calibrate a spectral OCT spectrometer using Doppler frequency. The technique of spectral calibration can be in principle adapted to of all kind of Fourier domain OCT devices.

Simultaneous analysis of flow velocity and spectroscopic properties of scattering media with the use of joint Spectral and Time domain OCT

The paper presents the way that colour can serve solving the problem of calibration points indexing in a camera geometrical calibration process. We propose a technique in which indexes of calibration points in a black-and-white chessboard are represented as sets of colour regions in the neighbourhood of calibration points. We provide some general rules for designing a colour calibration chessboard and provide a method of calibration image analysis. We show that this approach leads to obtaining better results than in the case of widely used methods employing information about already indexed points to compute indexes. We also report constraints concerning the technique. Nowadays we are witnessing an increasing need for camera geometrical calibration systems. They are vital for such applications as 3D modelling, 3D reconstruction, assembly control systems, etc. Wherever possible, calibration objects placed in the scene are used in a camera geometrical calibration process. This approach significantly increases accuracy of calibration results and makes the calibration data extraction process easier and universal. There are many geometrical camera calibration techniques for a known calibration scene [1]. A great number of them use as an input calibration points which are localised and indexed in the scene. In this paper we propose the technique of calibration points indexing which uses a colour chessboard. The presented technique was developed by solving problems we encountered during experiments with our earlier methods of camera calibration scene analysis [2]-[3]. In particular, the proposed technique increases the number of indexed points points in case of local lack of calibration points detection. At the beginning of the paper we present a way of designing a chessboard pattern. Then we describe a calibration point indexing method, and finally we show experimental results. A black-and-white chessboard is widely used in order to obtain sub-pixel accuracy of calibration points localisation [1]. Calibration points are defined as corners of chessboard squares. Assuming the availability of rough localisation of these points, the points can be indexed. Noting that differences in distances between neighbouring points in calibration scene images differ slightly, one of the local searching methods can be employed (e.g. [2]). Methods of this type search for a calibration point to be indexed, using a window of a certain size. The position of the window is determined by a vector representing the distance between two previously indexed points in the same row or column. However, experiments show that this approach has its disadvantages, as described below. * E-mail: A.Nowakowski@ire.pw.edu.pl Firstly, there is a danger of omitting some points during indexing in case of local lack of calibration points detection in a neighbourhood (e.g. caused by the presence of non-homogeneous light in the calibration scene). A particularly unfavourable situation is when the local lack of detection effects in the appearance of separated regions of detected calibration points. It is worth saying that such situations are likely to happen for calibration points situated near image borders. Such points are very important for the analysis of optical nonlinearities, and a lack of them can significantly influence the accuracy of distortion modelling. Secondly, such methods may give wrong results in the case of optical distortion with strong nonlinearities when getting information about the neighbouring index is not an easy task. Beside this, the methods are very sensitive to a single false localisation of a calibration point. Such a single false localisation can even result in false indexing of a big set of calibration points. To avoid the above-mentioned problems, we propose using a black-and-white chessboard which contains the coded index of a calibration point in the form of colour squares situated in the nearest neighbourhood of each point. The index of a certain calibration point is determined by colours of four nearest neighbouring squares (Fig.1). An order of squares in such foursome is important. Because the size of a colour square is determined only by the possibility of correct colour detection, the size of a colour square can be smaller than the size of a black or white square. The larger size of a black or white square is determined by the requirements of the exact localisation step which follows the indexing of calibration points [3]. In this step, edge information is extracted from a blackand-white chessboard. This edge information needs larger Artur Nowakowski, Wladyslaw Skarbek Institute of Radioelectronics, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warszawa, A.Nowakowski@ire.pw.edu.pl Received February 10, 2009; accepted March 27, 2009; published March 31, 2009 http://www.photonics.pl/PLP

A Method for Thiarubrine Canals Extraction in Optical Coherence Tomography Images of Schkuhria Pinnata Roots

Abstract This paper presents a method of automatic recognition of thiarubrine canals in images obtained with Optical Coherence Tomography technique. The plant material was the Ri-transformed root culture of South American herb Schkuhria pinnata. The series of highresolution OCT B-scans for the study were collected using custom made experimental system operating light of 800 nm central wavelength. The method reduces significant artefacts and uses region growing approach adapted to specific features of OCT images. Results of the identification have been compared with data obtained by specialist for selected B-scans. The algorithm accuracy was also verified using a simple numeric phantom.

True velocity mapping using joint spectral and time domain optical coherence tomography

We present both axial and transverse components estimation using joint Spectral and Time domain Optical Coherence Tomography (STdOCT) method. Whereas axial component of velocity vector can be determined from the time-dependent Doppler beating frequency, the transverse component can be assessed by the analysis of the broadening of flow velocity profiles (Doppler bandwidth). This enables us to quantitatively determine the absolute value of the velocity vector. The accurate analyses are performed using well-defined flow of Intralipid solution in the glass capillary. This enables performing in vivo imaging and allows to calculate velocity maps of the retinal vasculature.

Bessel beam OCM for analysis of global ischemia in mouse brain

We present the in-vivo imaging of the global mouse brain ischemia using Bessel beam optical coherence microscopy. This method allows to monitor changes in brain structure with extra control of blood flow during the process of artery occlusion. The results show the capability and sensitivity of OCM system with Bessel beam to analyze brain plasticity after severe injury within a period of 8 days.

Imaging of the stroke-related changes in the vascular system of the mouse brain with the use of extended focus Optical Coherence Microscopy

We used Optical Coherence Microscopy (OCM) to monitor structural and functional changes due to ischemic stroke in small animals brains in vivo. To obtain lateral resolution of 2.2 μm over the range of 600 μm we used extended focus configuration of OCM instrument involving Bessel beam. It provided access to detailed 3D information about the changes in brain vascular system up to the level of capillaries across I and II/III layers of neocortex. We used photothrombotic stroke model involving photoactive application of rose bengal to assure minimal invasiveness of the procedure and precise localization of the clot distribution center. We present the comparative analysis involving structural and angiographic maps of the stroke-affected brain enabling in-depth insight to the process of development of the disorder.

Wavelength to pixel calibration for FdOCT

We show that in Fourier domain Optical Coherence Tomography (FdOCT) it is possible to determine the wavelength of light for each point of the detected spectrum using any measurable physical quantity that has linear dependency on wavenumber. The presented approach is robust as the actual values of the measured quantity have no importance for the algorithm. As example we calibrate a SOCT spectrometer using Doppler frequency induced in time-dependent spectral fringes by a mirror moving in one of the arm of the interferometer. The results of calibration are validated using narrow spectral lines generated by optical parametric oscillator.