UNLABELLED: OpenSegSPIM is an open access and user friendly 3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data. The software is designed to extract, in a user-friendly way, quantitative relevant information from SPIM image stacks, such as the number of nuclei or cells. It provides quantitative measurement (volume, sphericity, distance, intensity) on Light Sheet Fluorescent Microscopy images. AVAILABILITY AND IMPLEMENTATION: freely available from http://www.opensegspim.weebly.com Source code and binaries under BSD License. CONTACT: [email protected] or [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The aim of this study is about tracing filamentary structures in both neuronal and retinal images. It is often crucial to identify single neurons in neuronal networks, or separate vessel tree structures in retinal blood vessel networks, in applications such as drug screening for neurological disorders or computer-aided diagnosis of diabetic retinopathy. Both tasks are challenging as the same bottleneck issue of filament crossovers is commonly encountered, which essentially hinders the ability of existing systems to conduct large-scale drug screening or practical clinical usage. To address the filament crossovers' problem, a two-step graph-theoretical approach is proposed in this paper. The first step focuses on segmenting filamentary pixels out of the background. This produces a filament segmentation map used as input for the second step, where they are further separated into disjointed filaments. Key to our approach is the idea that the problem can be reformulated as label propagation over directed graphs, such that the graph is to be partitioned into disjoint sub-graphs, or equivalently, each of the neurons (vessel trees) is separated from the rest of the neuronal (vessel) network. This enables us to make the interesting connection between the tracing problem and the digraph matrix-forest theorem in algebraic graph theory for the first time. Empirical experiments on neuronal and retinal image datasets demonstrate the superior performance of our approach over existing methods.

Neural stem cells and neural progenitors are early nervous system cells that form neurospheres when propagated in vitro. We study changes in growth using brightfield images to understand the effects of drugs. The image quality is generally poor, imposing challenges for automatic analysis. Level-set segmentation methods are able to handle topology changes but require close initializations for accurate and efficient results. Global level-set methods using single image-wide optimization objective functions are difficult to cope with large illumination and shading changes. We propose to adopt Hough transform to initialize localized level-sets for cell segmentation. Experimental results on 480 images with 738 neurospheres show that our proposed method performs best over existing level-set methods without appropriate initial contours.

The study of stem cells is one of the current most important biomedical research field. Understanding their development could allow multiple applications in regenerative medicine. For this purpose, we need automated methods for the segmentation and the modeling of neural stem cell development process into a neurosphere colony from phase contrast microscopy. We use such methods to extract relevant structural and textural features like cell division dynamism and cell behavior patterns for biological interpretation. The combination of phase contrast imaging, high fragility and complex evolution of neural stem cells pose many challenges in image processing and image analysis. This study introduces an on-line analysis method for the modeling of neurosphere evolution during the first three days of their development. From the corresponding time-lapse sequences, we extract information from the neurosphere using a combination of fast level set and curve detection for segmenting the cells. Then, based on prior biological knowledge, we generate possible and optimal 3-dimensional configuration using registration and evolutionary optimisation algorithm.

The rationale of our design is that although much of the literature of cooperative systems assumes perfect coherent detection, the assumption of having any channel estimates at the relays imposes an unreasonable burden on the relay station. Hence, non-coherently detected Reed-Solomon (ReS) coded Slow Frequency Hopping (SFH) assisted M-ary Frequency Shift Keying (FSK) is proposed for cooperative wireless networks, subjected to both partial-band interference and Rayleigh fading. Erasure insertion (EI) assisted ReS decoding based on the joint maximum output-ratio threshold test (MO-RTT) is investigated in order to evaluate the attainable system performance. Compared to the conventional error-correction-only decoder, the EI scheme may achieve an E_b/N_0 gain of approximately 3 dB at the Codeword Error Probability, P_w, of 10^{-4}, when employing the ReS(31,20) code combined with 32-FSK modulation. Additionally, we evaluated the system's performance, when either equal gain combining (EGC) or selection combining (SC) techniques are employed at the destination's receiver. The results demonstrated that in the presence of one and two assisting relays, the EGC scheme achieves gains of 1.5 dB and 1.0 dB at the P_w of 10^{-6}, respectively, compared to the SC arrangement. Furthermore, we demonstrated that for the same coding rate and packet size, the ReS(31,20) code using EI decoding is capable of outperforming convolutional coding, when 32-FSK modulation is considered, whilst LDPC coding had an edge over the above two schemes.

In this contribution, we employ the Mellin transform to derive the expressions for probability density function (PDF) of the product of Nakagami-m and Gamma distributed random variables. As the special cases of the Nakagami-m and Gamma family, the PDF of the product of Rayleigh distributed random variables and that of the product of exponentially distributed Random variables are also derived. We exploit the fact that the Mellin transform of a product of independent and identically distributed random variables is the product of the Mellin transforms of the individual random variables. Using this approach, the PDF of the product of random variables is expressed in the form of an easily computable infinite series. Furthermore, application of the PDFs in digital communications using M-ary orthogonal modulation is illustrated.

The rationale of our design is that although much of the literature of cooperative systems assumes perfect coherent detection, the assumption of having any channel estimates at the relays imposes an unreasonable burden on the relay station. Hence, non-coherently detected Reed-Solomon (ReS) coded Slow Frequency Hopping (SFH) assisted M-ary Frequency Shift Keying (FSK) is proposed for cooperative wireless networks, subjected to both partial-band interference and Rayleigh fading. Erasure insertion (EI) assisted ReS decoding based on the joint maximum output-ratio threshold test (MO-RTT) is investigated in order to evaluate the attainable system performance. Compared to the conventional error-correction-only decoder, the EI scheme may achieve a gain of approximately 3 dB at the Eb/N0of 10-4, when employing the ReS(31,20) code combined with 32-FSK modulation. Additionally, we evaluated the system's performance, when either equal gain combining (EGC) or selection combining (SC) techniques are employed at the destination's receiver. The results demonstrated that in the presence of one and two assisting relays, the EGC scheme achieves gains of 1.5 dB and 1.0 dB at the Eb/N0of 10-6, respectively, compared to the SC arrangement.

A convolutionally encoded noncoherent M-ary Frequency Shift Keying (MFSK) modulation scheme with diversity reception is considered. Soft metrics for Soft Decision Decoding (SDD) of noncoherent MFSK are derived assuming Rician channel model. Furthermore, the convergence behavior of the MFSK receiver is investigated using EXtrinsic Information Transfer (EXIT) charts. It has been demonstrated that the derived expressions for soft information are useful allowing SDD of the MFSK scheme exploiting diversity and the EXIT chart analysis provides useful insights into its iterative decoding behavior.

A convolutionally encoded noncoherent M-ary Frequency Shift Keying (MFSK) modulation scheme using diversity reception is considered. A novel technique of generating soft information for Soft Decision Decoding (SDD) of noncoherent MFSK is derived assuming various channel models. Furthermore, the convergence behavior of the MFSK receiver is investigated using Extrinsic Information Transfer (EXIT) charts. It is demonstrated that the expressions derived for SDD of the MFSK scheme are useful for exploiting the beneficial effects of diversity. We also demonstrate that EXIT chart analysis provides accurate insights into the system's iterative decoding behavior.

Serially concatenated and iteratively decoded Irregular Variable Length Coding (IrVLC) combined with preceded Fast Frequency Hopping (FFH) M-ary Frequency Shift Keying (MFSK) is considered. We employ Extrinsic Information Transfer (EXIT) charts to investigate the 3-stage concatenation of the FFH-MFSK demodulator, the rate-1 decoder and the outer IrVLC decoder. The proposed joint source and channel coding scheme is capable of operating at low Signal-to-Noise Ratio (SNR) in Rayleigh fading channels contaminated by Partial Band Noise Jamming (PBNJ). The IrVLC scheme is comprised of a number of component Variable Length Coding (VLC) codebooks employing different coding rates for encoding particular fractions of the input source symbol stream. These fractions may be chosen with the aid of EXIT charts in order to shape the inverted EXIT curve of the IrVLC codec so that it can be matched with the EXIT curve of the inner decoder. We demonstrate that using the proposed scheme an inflnitesimally low bit error ratio may be achieved at low SNR values.

Serially concatenated and iteratively decoded irregular variable length coding (IrVLC) combined with preceded fast frequency hopping (FFH) M-ary frequency shift keying (MFSK) is considered. The proposed joint source and channel coding scheme is capable of low signal-to-noise ratio (SNR) operation in Rayleigh fading channels contaminated by partial band noise jamming (PBNJ). The IrVLC scheme is comprised of a number of component variable length coding (VLC) codebooks employing different coding rates for encoding particular fractions of the input source symbol stream. These fractions may be chosen with the aid of extrinsic information transfer (EXIT) charts in order to shape the inverted EXIT curve of the IrVLC codec so that it can be matched with the EXIT curve of the inner decoder. We demonstrate that using the proposed scheme near-zero bit error ratio may be achieved at low SNR values and the IrVLC based scheme yields a further gain of up to 0.3 dB over the identical-rate single-class VLC based benchmarker scheme

We propose a novel bit error ratio (BER) analysis technique for fast frequency hopping (FFH) assisted M-ary frequency shift keying (MFSK) using product combining (PC), when the channel is contaminated by partial band noise jamming (PBNJ). Exploiting the fact that the Mellin transform of the product of independent random variables is the product of their Mellin transforms, we derive the probability density function (PDF) of the PC's output, when communicating in uncorrelated Rayleigh fading channels contaminated by PBNJ. The derivation of the PDF thus allows computation of the system's BER. It is shown that the Mellin transform substantially simplifies the analysis of the PC receiver and facilitates for the first time the analysis of FFH-MFSK PC receiver for modulation orders of M > 2.

In this contribution, soft-input-soft-output (SISO) decoding aided successive interference cancellation (SIC) is considered in fast frequency hopping (FFH), M-ary frequency shift keying (MFSK) using product combining (PC), when operating in multiple access (MA) Nakagami-m channels. All users' M-ary source symbols are encoded using non-binary LDPC codes and the encoded symbols are transmitted using FFH-MFSK modulation. A sub-optimum soft metric is proposed which is based on self-normalization of the diversity combiner outputs. In the context of the proposed SIC scheme, the receiver exploits the soft information fed back by the LDPC decoder to the demodulator in order to cancel the interference imposed by the reliably detected symbols. Our simulation results show that the proposed scheme is capable of combatting the effects of multiuser interference and outperforms conventional iterative decoding by about 1 dB.

Iterative decoding (ID) aided fast frequency hopping (FFH), M-ary frequency shift keying (MFSK) using clipped combining in multiple access (MA) channels is investigated. All users' data are convolutionally encoded and the encoded bits are interleaved and converted to M-ary symbols, which are transmitted using FFH-MFSK modulation. The soft metrics to be passed from the demodulator to the decoder are derived assuming a Rayleigh fading channel. We also propose a novel multiuser detection (MUD) scheme which employs joint soft decoding as well as successive interference cancellation (SIC), the receiver exploiting the soft information fed back by the decoder to the demodulator in order to cancel the interference imposed by reliable symbols. Our simulation results show that the proposed scheme is capable of combatting multiuser interference and outperforms the conventional ID by about 3dB.

In this contribution, we analyze the bit error rate (BER) performance of fast frequency hopping (FFH) assisted M-ary frequency shift keying (MFSK) using product combining. Product combining constitutes an efficient yet low-complexity scheme that may be employed in FFH-MFSK receiver to combat the detrimental effects of interference or jamming. We propose a novel approach to the analysis of this receiver system, which is based on the Mellin transform. Using this approach, the probability density function (PDF) of the product combiner output is expressed in a closed form. Based on the resultant PDF, the BER of the FFH-MFSK product combining receiver operating in Rayleigh fading channel is evaluated analytically. It is shown that the Mellin transform simplifies the analysis of the product combining receiver.

In this contribution, we propose two successive interference cancellation (SIC) schemes for a fast frequency hopping (FFH) multiple access (MA) system using M-ary frequency shift keying (MFSK) and invoking multi-user detection (MUD). One of the proposed schemes invokes clipped combining, while the other scheme employs both product combining and clipped combining. The SIC schemes are adapted from a scheme proposed by U.-C. Fiebig in 1996. The basic principle of the SIC schemes is that detection is carried out in multiple stages and during each stage, only the most reliable symbols are detected. In subsequent stages, the interference contributed by the already detected symbols may be removed. The performance of the proposed schemes is evaluated and compared to that of Fiebig's scheme, when the FFH-MFSK system operates in a Nakagami-m fading MA channel. The simulation results demonstrate that the proposed schemes attain a better bit error rate performance than Fiebig's scheme.

In this treatise we demonstrate, how a high spatial and frequency diversity can be achieved by combining differential space-time block coding (DSTBC) and fast frequency hopping (FFH). The proposed FFH assisted DSTBC scheme is capable of achieving a high diversity order given by the product of the frequency diversity order achieved by FFH and by the spatial diversity order offered by the DSTBC arrangement. Hence, the system is capable of exploiting the advantages of both DSTBC and FFH. Furthermore it is less vulnerable to some of their individual disadvantages, such as the performance degradation of DSTBC due to fast fading and the large bandwidth requirement of the FFH system. The proposed system also benefits from the employment of sphere packing and iterative turbo detection