Use of Autostitch for automatic stitching of microscope images

Organellar genomic characterization of Anunuuluaehu liula representing a new genus and species of Phyllophoraceae (Gigartinales, Rhodophyta) from the mesophotic zone of Hawai'i

Over the last 2 decades, routine collections in the Hawaiian Archipelago have expanded to mesophotic reefs, leading to the discovery of a new red algal genus and species, here described as Anunuuluaehu liula gen. et sp. nov. This study provides a detailed genus and species description and characterizes chloroplast and mitochondrial organellar genomes. The new genus, Anunuuluaehu, shares many characteristics with the family Phyllophoraceae and shows close similarities to Archestennogramma and Stenogramma, including habit morphology, nemathecia forming proliferations at the outer cortex with terminal chains of tetrasporangia, and carposporophytes with multi-layered pericarps. The single species in this genus exhibits distinctive features within the Phyllophoraceae: the presence of single-layer construction of large medullary cells and the development of long, tubular gonimoblastic filaments. Multi-gene phylogenetic analyses confirmed it as a unique, monophyletic lineage within the family. Cis-splicing genes, interrupted by intron-encoded proteins within group II introns, are present in both the chloroplast and mitochondrial genomes of A. liula. Notably, a specific region of the coxI group II intron exhibits similarity to fungal introns. Anunuuluaehu liula is presumed to be endemic to the Hawaiian Archipelago and thus far is known to live solely at mesophotic depths from Hōlanikū to Kaho'olawe ranging from 54 to 201 m, which is the deepest collection record of any representative in the family. Overall, this study enhances our understanding of the genomic and taxonomic complexities of red algae in mesophotic habitats, emphasizing the significance of continued research in this area to uncover further insights into evolutionary processes and biogeographic patterns.

Large-scale time-lapse scanning electron microscopy image mosaic using a smooth stitching strategy

Due to the trade-off between the field of view and resolution of various microscopes, obtaining a wide-view panoramic image through high-resolution image tiles is frequently encountered and demanded in numerous applications. Here, we propose an automatic image mosaic strategy for sequential 2D time-lapse scanning electron microscopy (SEM) images. This method can accurately compute pairwise translations among serial image tiles with indeterminate overlapping areas. The detection and matching of feature points are limited by geographical coordinates, thus avoiding accidental mismatching. Moreover, the nonlinear deformation of the mosaic part is also taken into account. A smooth stitching field is utilized to gradually transform the perspective transformation in overlapping regions into the linear transformation in non-overlapping regions. Experimental results demonstrate that better image stitching accuracy can be achieved compared with some other image mosaic algorithms. Such a method has potential applications in high-resolution large-area analysis using serial microscopy images. RESEARCH HIGHLIGHTS: An automatic image mosaic strategy for processing sequential scanning electron microscopy images is proposed. A smooth stitching field is applied in the image mosaic. Improved stitching accuracy is achieved compared with other conventional mosaic methods.

Fast and stable Fourier ptychographic microscopy based on improved phase recovery strategy

Fourier ptychographic microscopy (FPM) imaging is a computational imaging technology that can reconstruct wide-field high-resolution (HR) images. It uses a series of low-resolution images captured by a camera under different illumination angles. The images are stitched in the Fourier domain to expand their spectral range. Under high-angle illumination, a dark-field image is noisy with a low signal-to-noise ratio, which significantly reduces the reconstruction quality of FPM. Conventional reconstruction algorithms often have low FPM imaging performance and efficiency due to optimization strategies. In response to these problems, this paper proposes an FPM imaging method based on an improved phase recovery strategy to optimize the alternating iterative algorithm. The technique uses an improved threshold method to reduce noise in the image preprocessing stage to maximize the retention of high-frequency sample information. Moreover, an adaptive control factor is added in the subsequent iterative update process to balance the sample spectrum function. This study verifies the effectiveness of the proposed method on both simulation and experimental images. The results show that the proposed method can effectively suppress image background noise and has a faster convergence speed and higher robustness. In addition, it can be used to reconstruct HR complex amplitude images of objects under wide field-of-view conditions.

Recording of Long Low-Amplitude Bulk Elastic Waves in Transparent Solid Waveguides by Digital and Classical Holography

In this paper we compare two implementations of the holographic technique for recording long, nonlinear, elastic waves of low amplitude in solid polymer waveguides: classical holographic interferometry and digital holography. Both implementations are realized in transmission configuration, with recording in the off-axis schematic. The advantages and disadvantages of these implementations are discussed as applied to the investigation of the evolution of shock waves and strain solitons in transparent solid waveguides.

Optical scanning Fourier ptychographic microscopy

We propose a lower-cost and practical active scanning optical scanning Fourier ptychographic microscopy (OSFPM). Featured is a simple setup of Galvo mirrors capable of scanning large-sized objects. The active scanning laser beam is projected onto the sample in a circular pattern to form multiple lower-resolution images. With multiple lower-resolution images, a higher-resolution image is subsequently reconstructed. The OSFPM is able to more precisely control the overlap of the incident light illumination as compared to that in conventional LED-based or other laser-based scanning FPM systems. The proposed microscope is also suitable for applications where a larger size of the object needs to be imaged with efficient illumination.

NMDA receptor-dependent signalling pathways regulate arginine vasopressin expression in the paraventricular nucleus of the rat

The antidiuretic hormone arginine vasopressin (AVP) regulates water homeostasis, blood pressure and a range of stress responses. It is synthesized in the hypothalamus and released from the posterior pituitary into the general circulation upon a range of stimuli. While the mechanisms leading to AVP secretion have been widely investigated, the molecular mechanisms regulating AVP gene expression are mostly unclear. Here we investigated the neurotransmitters and signal transduction pathways that activate AVP gene expression in the paraventricular nucleus (PVN) of the rat using acute brain slices and quantitative real-time PCR. We show that stimulation with l-glutamate robustly induced AVP gene expression in acute hypothalamic brain slices containing the PVN. More specifically, we show that AVP transcription was stimulated by NMDA. Using pharmacological treatments, our data further reveal that the activation of ERK1/2 (PD184352), CaMKII (KN-62) and PI3K (LY294002; 740 Y-P) is involved in the NMDA-induced AVP gene expression in the PVN. Together, this study identifies NMDA-mediated cell signalling pathways that regulate AVP gene expression in the rat PVN.

Automated stitching of microscope images of fluorescence in cells with minimal overlap

The morphology of tumor cells is highly related to their phenotype and activity. To verify the drug response of a brain tumor patient, fluorescence microscope images of drug-treated patient-derived cells in each well are analyzed. Due to the limitation of the field of view (FOV), a large number of small FOVs are acquired to compose one complete microscope well. Here, we propose an automated method for accurately stitching tile-scanned fluorescence microscope images, even with noise and a narrow overlapping region between adjacent fields. The proposed method is based on intensity-based normalized cross-correlation (NCC) and a triangular method-based threshold. The proposed method's quantitative accuracy and the sensitivity of the input was compared to other existing stitching tools, MIST and FijiIS, setting manually stitched images as the ground truth. The test images were 20 samples of 3 × 3 grid images in three versions of the fluorescence channel. The distance between the location of each field and number of cells was determined for different input field overlap ranges (1%, 3%, 5%, and 10%), while the actual value was about 1.15%. The proposed method had a distance error of 1.5 pixels at an input overlap of 1%, showing the lowest minimum error at all channels. Regarding the difference in cell numbers, although the number of overlapping cells was always small because of the narrow overlapping range, the proposed method was able to generate the resultant image with the smallest difference. In addition, to confirm the size limitation of the proposed algorithm, the accuracy of stitching images of grid structures 3 × 3, 5 × 5, 10 × 10-20 × 20 was tested, showing consistent results. In conclusion, quantitative evaluation of the performance of the method proved its improved accuracy compared to other current state-of-art techniques, and it showed robust performance even with noise and a narrow overlapping region between adjacent fields.

Digital, Rapid, Accurate, and Label-Free Enumeration of Viable Microorganisms Enabled by Custom-Built On-Glass-Slide Culturing Device and Microscopic Scanning

Accurately measuring the number of viable microorganisms plays an essential role in microbiological studies. Since the conventional agar method of enumerating visible colonies is time-consuming and not accurate, efforts have been made towards overcoming these limitations by counting the invisible micro-colonies. However, none of studies on micro-colony counting was able to save significant time or provide accurate results. Herein, we developed an on-glass-slide cell culture device that enables rapid formation of micro-colonies on a 0.38 mm-thick gel film without suffering from nutrient and oxygen deprivation during bacteria culturing. Employing a phase contrast imaging setup, we achieved rapid microscopic scanning of micro-colonies within a large sample area on the thin film without the need of fluorescent staining. Using Escherichia coli (E. coli) as a demonstration, our technique was able to shorten the culturing time to within 5 h and automatically enumerate the micro-colonies from the phase contrast images. Moreover, this method delivered more accurate counts than the conventional visible colony counting methods. Due to these advantages, this imaging-based micro-colony enumeration technique provides a new platform for the quantification of viable microorganisms.

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows

Designing applications for scalability is key to improving their performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with data dependencies, memory management, data motion, and processor occupancy. The Hybrid Task Graph Scheduler (HTGS) improves programmer productivity when implementing hybrid workflows for multi-core and multi-GPU systems. The Hybrid Task Graph Scheduler (HTGS) is an abstract execution model, framework, and API that increases programmer productivity when implementing hybrid workflows for such systems. HTGS manages dependencies between tasks, represents CPU and GPU memories independently, overlaps computations with disk I/O and memory transfers, keeps multiple GPUs occupied, and uses all available compute resources. Through these abstractions, data motion and memory are explicit; this makes data locality decisions more accessible. To demonstrate the HTGS application program interface (API), we present implementations of two example algorithms: (1) a matrix multiplication that shows how easily task graphs can be used; and (2) a hybrid implementation of microscopy image stitching that reduces code size by ≈ 43% compared to a manually coded hybrid workflow implementation and showcases the minimal overhead of task graphs in HTGS. Both of the HTGS-based implementations show good performance. In image stitching the HTGS implementation achieves similar performance to the hybrid workflow implementation. Matrix multiplication with HTGS achieves 1.3× and 1.8× speedup over the multi-threaded OpenBLAS library for 16k × 16k and 32k × 32k size matrices, respectively.

Adaptive pixel-super-resolved lensfree in-line digital holography for wide-field on-chip microscopy

High-resolution wide field-of-view (FOV) microscopic imaging plays an essential role in various fields of biomedicine, engineering, and physical sciences. As an alternative to conventional lens-based scanning techniques, lensfree holography provides a new way to effectively bypass the intrinsical trade-off between the spatial resolution and FOV of conventional microscopes. Unfortunately, due to the limited sensor pixel-size, unpredictable disturbance during image acquisition, and sub-optimum solution to the phase retrieval problem, typical lensfree microscopes only produce compromised imaging quality in terms of lateral resolution and signal-to-noise ratio (SNR). Here, we propose an adaptive pixel-super-resolved lensfree imaging (APLI) method which can solve, or at least partially alleviate these limitations. Our approach addresses the pixel aliasing problem by Z-scanning only, without resorting to subpixel shifting or beam-angle manipulation. Automatic positional error correction algorithm and adaptive relaxation strategy are introduced to enhance the robustness and SNR of reconstruction significantly. Based on APLI, we perform full-FOV reconstruction of a USAF resolution target (~29.85 mm²) and achieve half-pitch lateral resolution of 770 nm, surpassing 2.17 times of the theoretical Nyquist–Shannon sampling resolution limit imposed by the sensor pixel-size (1.67µm). Full-FOV imaging result of a typical dicot root is also provided to demonstrate its promising potential applications in biologic imaging.

Panoramic-reconstruction temporal imaging for seamless measurements of slowly-evolved femtosecond pulse dynamics

Single-shot real-time characterization of optical waveforms with sub-picosecond resolution is essential for investigating various ultrafast optical dynamics. However, the finite temporal recording length of current techniques hinders comprehensive understanding of many intriguing ultrafast optical phenomena that evolve over a timescale much longer than their fine temporal details. Inspired by the space-time duality and by stitching of multiple microscopic images to achieve a larger field of view in the spatial domain, here a panoramic-reconstruction temporal imaging (PARTI) system is devised to scale up the temporal recording length without sacrificing the resolution. As a proof-of-concept demonstration, the PARTI system is applied to study the dynamic waveforms of slowly evolved dissipative Kerr solitons in an ultrahigh-Q microresonator. Two 1.5-ns-long comprehensive evolution portraits are reconstructed with 740 fs resolution and dissipative Kerr soliton transition dynamics, in which a multiplet soliton state evolves into a stable singlet soliton state, are depicted.Real-time characterization of ultrafast dynamics comes with a tradeoff between temporal resolution and recording length. Here, Li et al. use a temporal reconstruction technique inspired by panoramic microscopy to image the dynamics of slowly evolved dissipative Kerr solitons in a microresonator.

Radiography registration for mosaic tomography

A hybrid method of stitching X-ray computed tomography (CT) datasets is proposed and the feasibility to apply the scheme in a synchrotron tomography beamline with micrometre resolution is shown. The proposed method enables the field of view of the system to be extended while spatial resolution and experimental setup remain unchanged. The approach relies on taking full tomographic datasets at different positions in a mosaic array and registering the frames using Fourier phase correlation and a residue-based correlation. To ensure correlation correctness, the limits for the shifts are determined from the experimental motor position readouts. The masked correlation image is then minimized to obtain the correct shift. The partial datasets are blended in the sinogram space to be compatible with common CT reconstructors. The feasibility to use the algorithm to blend the partial datasets in projection space is also shown, creating a new single dataset, and standard reconstruction algorithms are used to restore high-resolution slices even with a small number of projections.

Resolution-enhanced Fourier ptychographic microscopy based on high-numerical-aperture illuminations

High-resolution and wide field-of-view (FOV) microscopic imaging plays a central role in diverse applications such as high-throughput screening and digital pathology. However, conventional microscopes face inherent trade-offs between the spatial resolution and FOV, which are fundamental limited by the space-bandwidth product (SBP) of the optical system. The resolution-FOV tradeoff can be effectively decoupled in Fourier ptychography microscopy (FPM), however, to date, the effective imaging NA achievable with a typical FPM system is still limited to the range of 0.4–0.7. Herein, we report, for the first time, a high-NA illumination based resolution-enhanced FPM (REFPM) platform, in which a LED-array-based digital oil-immersion condenser is used to create high-angle programmable plane-wave illuminations, endowing a 10×, 0.4 NA objective lens with final effective imaging performance of 1.6 NA. With REFPM, we present the highest-resolution results with a unprecedented half-pitch resolution of 154 nm at a wavelength of 435 nm across a wide FOV of 2.34 mm², corresponding to an SBP of 98.5 megapixels (~50 times higher than that of the conventional incoherent microscope with the same resolution). Our work provides an important step of FPM towards high-resolution large-NA imaging applications, generating comparable resolution performance but significantly broadening the FOV of conventional oil-immersion microscopes.

Cancer multicellular spheroids: volume assessment from a single 2D projection

Volume is one of the most important features for the characterization of a tumour on a macroscopic scale. It is often used to assess the effectiveness of care treatments, thus making its correct evaluation a crucial issue for patient care. Similarly, volume is a key feature on a microscopic scale. Multicellular cancer spheroids are 3D tumour models widely employed in pre-clinical studies to test the effects of drugs and radiotherapy treatments. Very few methods have been proposed to estimate the tumour volume arising from a 2D projection of multicellular spheroids, and even fewer have been designed to provide a 3D reconstruction of the tumour shape. In this work, we propose Reconstruction and Visualization from a Single Projection (ReViSP), an automatic method conceived to reconstruct the 3D surface and estimate the volume of single cancer multicellular spheroids, or even of spheroid cultures. As the input parameter ReViSP requires only one 2D projection, which could be a widefield microscope image. We assessed the effectiveness of our method by comparing it with other approaches. To this purpose, we used a new strategy that allowed us to achieve accurate volume measurements based on the analysis of home-made 3D objects, built by mimicking the spheroid morphology. The results confirmed the effectiveness of our method for both 3D reconstruction and volume assessment. ReViSP software is distributed as an open source tool.

Digital image processing and analysis for activated sludge wastewater treatment

Activated sludge system is generally used in wastewater treatment plants for processing domestic influent. Conventionally the activated sludge wastewater treatment is monitored by measuring physico-chemical parameters like total suspended solids (TSSol), sludge volume index (SVI) and chemical oxygen demand (COD) etc. For the measurement, tests are conducted in the laboratory, which take many hours to give the final measurement. Digital image processing and analysis offers a better alternative not only to monitor and characterize the current state of activated sludge but also to predict the future state. The characterization by image processing and analysis is done by correlating the time evolution of parameters extracted by image analysis of floc and filaments with the physico-chemical parameters. This chapter briefly reviews the activated sludge wastewater treatment; and, procedures of image acquisition, preprocessing, segmentation and analysis in the specific context of activated sludge wastewater treatment. In the latter part additional procedures like z-stacking, image stitching are introduced for wastewater image preprocessing, which are not previously used in the context of activated sludge. Different preprocessing and segmentation techniques are proposed, along with the survey of imaging procedures reported in the literature. Finally the image analysis based morphological parameters and correlation of the parameters with regard to monitoring and prediction of activated sludge are discussed. Hence it is observed that image analysis can play a very useful role in the monitoring of activated sludge wastewater treatment plants.

Improving reliability of live/dead cell counting through automated image mosaicing

Cell counting is one of the basic needs of most biological experiments. Numerous methods and systems have been studied to improve the reliability of counting. However, at present, manual cell counting performed with a hemocytometer still represents the gold standard, despite several problems limiting reproducibility and repeatability of the counts and, at the end, jeopardizing their reliability in general. We present our own approach based on image processing techniques to improve counting reliability. It works in two stages: first building a high-resolution image of the hemocytometer's grid, then counting the live and dead cells by tagging the image with flags of different colours. In particular, we introduce GridMos (http://sourceforge.net/p/gridmos), a fully-automated mosaicing method to obtain a mosaic representing the whole hemocytometer's grid. In addition to offering more significant statistics, the mosaic "freezes" the culture status, thus permitting analysis by more than one operator. Finally, the mosaic achieved can thus be tagged by using an image editor, thus markedly improving counting reliability. The experiments performed confirm the improvements brought about by the proposed counting approach in terms of both reproducibility and repeatability, also suggesting the use of a mosaic of an entire hemocytometer's grid, then labelled trough an image editor, as the best likely candidate for the new gold standard method in cell counting.

Lipid vesicle shape analysis from populations using light video microscopy and computer vision

We present a method for giant lipid vesicle shape analysis that combines manually guided large-scale video microscopy and computer vision algorithms to enable analyzing vesicle populations. The method retains the benefits of light microscopy and enables non-destructive analysis of vesicles from suspensions containing up to several thousands of lipid vesicles (1–50 µm in diameter). For each sample, image analysis was employed to extract data on vesicle quantity and size distributions of their projected diameters and isoperimetric quotients (measure of contour roundness). This process enables a comparison of samples from the same population over time, or the comparison of a treated population to a control. Although vesicles in suspensions are heterogeneous in sizes and shapes and have distinctively non-homogeneous distribution throughout the suspension, this method allows for the capture and analysis of repeatable vesicle samples that are representative of the population inspected.

Accurate three-dimensional virtual reconstruction of surgical field using calibrated trajectories of an image-guided medical robot

Brain tumor margin removal is challenging because diseased tissue is often visually indistinguishable from healthy tissue. Leaving residual tumor leads to decreased survival, and removing normal tissue causes life-long neurological deficits. Thus, a surgical robotics system with a high degree of dexterity, accurate navigation, and highly precise resection is an ideal candidate for image-guided removal of fluorescently labeled brain tumor cells. To image, we developed a scanning fiber endoscope (SFE) which acquires concurrent reflectance and fluorescence wide-field images at a high resolution. This miniature flexible endoscope was affixed to the arm of a RAVEN II surgical robot providing programmable motion with feedback control using stereo-pair surveillance cameras. To verify the accuracy of the three-dimensional (3-D) reconstructed surgical field, a multimodal physical-sized model of debulked brain tumor was used to obtain the 3-D locations of residual tumor for robotic path planning to remove fluorescent cells. Such reconstruction is repeated intraoperatively during margin clean-up so the algorithm efficiency and accuracy are important to the robotically assisted surgery. Experimental results indicate that the time for creating this 3-D surface can be reduced to one-third by using known trajectories of a robot arm, and the error from the reconstructed phantom is within 0.67 mm in average compared to the model design.

Automated image mosaics by non-automated light microscopes: the MicroMos software tool

Light widefield microscopes and digital imaging are the basis for most of the analyses performed in every biological laboratory. In particular, the microscope's user is typically interested in acquiring high-detailed images for analysing observed cells and tissues, meanwhile being representative of a wide area to have reliable statistics. The microscopist has to choose between higher magnification factor and extension of the observed area, due to the finite size of the camera's field of view. To overcome the need of arrangement, mosaicing techniques have been developed in the past decades for increasing the camera's field of view by stitching together more images. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Or alternatively, the methods are conceived just to provide visually pleasant mosaics not suitable for quantitative analyses. This work presents a tool for building mosaics of images acquired with nonautomated light microscopes. The method proposed is based on visual information only and the mosaics are built by incrementally stitching couples of images, making the approach available also for online applications. Seams in the stitching regions as well as tonal inhomogeneities are corrected by compensating the vignetting effect. In the experiments performed, we tested different registration approaches, confirming that the translation model is not always the best, despite the fact that the motion of the sample holder of the microscope is apparently translational and typically considered as such. The method's implementation is freely distributed as an open source tool called MicroMos. Its usability makes building mosaics of microscope images at subpixel accuracy easier. Furthermore, optional parameters for building mosaics according to different strategies make MicroMos an easy and reliable tool to compare different registration approaches, warping models and tonal corrections.

Adipose-derived stem cells seeded on acellular dermal matrix grafts enhance wound healing in a murine model of a full-thickness defect

INTRODUCTION

The promotion of wound healing using dermal substitutes has become increasingly widespread, but the outcomes of substitute-assisted healing remain functionally deficient. Adipose-derived stem cells (ASCs) have been investigated widely in regenerative medicine and tissue engineering, and they have the potential to enhance wound healing. In this study, we focused on investigating the effects and mechanism of ASCs combined with an acellular dermal matrix (ADM) to treat full-thickness cutaneous wounds in a murine model.

METHODS

The ADM was prepared from the dorsal skin of nude mice by decellularization by treatment with trypsin followed by Triton X-100. The human ASCs were isolated and cultured from abdominal lipoaspirate. We created a rounded, 8-mm, full-thickness cutaneous wound in nude mice and divided the mice into the following 4 groups: silicon sheet cover only, silicon sheet with spreading ASCs, ADM only, and ASCs seeded on ADM. The granulation thickness was evaluated by histology after 7 days. Further comparisons between the ADM only and ASC-seeded ADM groups were undertaken by assessing the reepithelialization ratio and blood vessel density at postoperative days 9 and 14. Statistical analyses were conducted using Student 2-tailed t test. Immunofluorescent histology and ASC labeling were also performed to identify possible mechanisms.

RESULTS

The ADM was successfully prepared, and the cytometry analysis and differentiation assay provided the characterization of the human ASCs. A marked improvement in granulation thickness was detected in the ADM-ASC group in comparison with other 3 groups. A significantly increased rate of reepithelialization in the ADM-ASC group (80 ± 6%) compared to the ADM only group (60 ± 7%) was noted on postoperative day 9. The blood vessel density was evidently increased in the ADM-ASC group (7.79 ± 0.40 vessels per field) compared to the ADM only group (5.66 ± 0.23 vessels) on day 14. Cell tracking experiments demonstrated that labeled ASCs were colocalized with staining for VEGF or endothelial cell maker vWF after the transplantation of ADM-ASCs on postoperative day 14.

CONCLUSIONS

Adipose-derived stem cells seeded on an ADM can enhance wound healing, promote angiogenesis, and contribute to newly formed vasculature, and VEGF-expressing ASCs can be detected after transplantation. This model could be used to improve the other clinical applications of ASCs and to decipher the detailed mechanism by which ASCs interact with wound tissue.

Creating a virtual slide map from sputum smear images for region-of-interest localisation in automated microscopy

We address the location of regions-of-interest in previously scanned sputum smear slides requiring re-examination in automated microscopy for tuberculosis (TB) detection. We focus on the core component of microscope auto-positioning, which is to find a point of reference, position and orientation, on the slide so that it can be used to automatically bring desired fields to the field-of-view of the microscope. We use virtual slide maps together with geometric hashing to localise a query image, which then acts as the point of reference. The true positive rate achieved by the algorithm was above 88% even for noisy query images captured at slide orientations up to 26°. The image registration error, computed as the average mean square error, was less than 14 pixel² (corresponding to 1.02 μm²). The algorithm is inherently robust to changes in slide orientation and placement and showed high tolerance to illumination changes and robustness to noise.

Quantitative analysis of BDNF/TrkB protein and mRNA in cortical and striatal neurons using α-tubulin as a normalization factor

The neurotrophin brain-derived neurotrophic factor (BDNF) and its receptor tyrosine kinase TrkB serve important regulatory roles for multiple aspects of the biology of neurons including cell death, survival, growth, differentiation, and plasticity. Regulation of the local availability of BDNF/TrkB at distinct subcellular domains such as soma, dendrites, axons, growth cones, nerve terminals, and spines appears to contribute to their specific functions. In view of the variance in size and shape of neurons and their compartments, previous quantitative studies of the BDNF/TrkB protein and mRNA lacked a robust normalization procedure. To overcome this problem, we have established methods that use immunofluorescence detection of α-tubulin as a normalization factor for the quantitative analysis of protein and mRNA in primary rat cortical and striatal neurons in culture. The efficacy of this approach is demonstrated by studying the dynamic distribution of proteins and mRNA at different growth stages or conditions. Treatment of cultured neurons with KCl resulted in increased levels of TrkB protein, reduced levels of BDNF mRNA (composite of multiple transcripts) and a slight reduction in BDNF protein levels in the dendrites from the cortex. The KCl treatment also lowered the percentage of BDNF and TrkB proteins in the soma indicative of protein transport. Finally, analysis of the rat cortical and striatal neurons demonstrated comparable or even higher levels of BDNF/TrkB protein and BDNF mRNA in the neurons from the striatum. Thus, in contrast to previous observations made in vivo, striatal neurons are capable of synthesizing BDNF mRNA when cultured in growth media in vitro. The analytical approach presented here provides a detailed understanding of BDNF/TrkB levels in response to a variety of neuronal activities. Our methods could be used broadly, including applications in cell and tissue cytometry, to yield accurate quantitative data of gene expression in cellular and subcellular contexts. © 2012 International Society for Advancement of Cytometry.

Creating a virtual slide map of sputum smears by auto-stitching

Under a microscope, only a small field of a slide can be seen through the eye piece. A digital replication of a large section of the smear on a slide is desirable for several applications, including image-based auto-positioning for automated microscopy and telepathology. To achieve this, images of the various fields on the slide can be captured and stitched automatically to form a virtual slide map. We compared two auto-stitching methods, namely the geometric hashing and the scale invariant feature transform (SIFT), applied to images of tuberculosis-infected sputum smears. Experimental results show good agreement between the two methods.

HistoStitcher(©): an interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments

We present an interactive program called HistoStitcher(©) for accurate and rapid reassembly of histology fragments into a pseudo-whole digitized histological section. HistoStitcher(©) provides both an intuitive graphical interface to assist the operator in performing the stitch of adjacent histology fragments by selecting pairs of anatomical landmarks, and a set of computational routines for determining and applying an optimal linear transformation to generate the stitched image. Reconstruction of whole histological sections from images of slides containing smaller fragments is required in applications where preparation of whole sections of large tissue specimens is not feasible or efficient, and such whole mounts are required to facilitate (a) disease annotation and (b) image registration with radiological images. Unlike manual reassembly of image fragments in a general purpose image editing program (such as Photoshop), HistoStitcher(©) provides memory efficient operation on high resolution digitized histology images and a highly flexible stitching process capable of producing more accurate results in less time. Further, by parameterizing the series of transformations determined by the stitching process, the stitching parameters can be saved, loaded at a later time, refined, or reapplied to multi-resolution scans, or quickly transmitted to another site. In this paper, we describe in detail the design of HistoStitcher(©) and the mathematical routines used for calculating the optimal image transformation, and demonstrate its operation for stitching high resolution histology quadrants of a prostate specimen to form a digitally reassembled whole histology section, for 8 different patient studies. To evaluate stitching quality, a 6 point scoring scheme, which assesses the alignment and continuity of anatomical structures important for disease annotation, is employed by three independent expert pathologists. For 6 studies compared with this scheme, reconstructed sections generated via HistoStitcher(©) scored higher than reconstructions generated by an expert pathologist using Photoshop.

Neuroprotective effects of granulocyte-colony stimulating factor in a novel transgenic mouse model of SCA17

Spinocerebellar ataxia type 17 (SCA17) is an autosomal dominant inherited disorder characterized by degeneration of spinocerebellar tracts and selected brainstem neurons owing to the expansion of a CAG repeat of the human TATA-binding protein (hTBP) gene. To gain insight into the pathogenesis of this hTBP mutation, we generated transgenic mice with the mutant hTBP gene driven by the Purkinje specific protein (Pcp2/L7) gene promoter. Mice with the expanded hTBP allele developed ataxia within 2-5 months. Behavioral analysis of L7-hTBP transgenic mice showed reduced fall latency in a rotarod assay. Purkinje cell degeneration was identified by immunostaining of calbindin and IP3R1. Reactive gliosis and neuroinflammation occurred in the transgenic cerebellum, accompanied by up-regulation of GFAP and Iba1. The L7-hTBP transgenic mice were thus confirmed to recapitulate the SCA17 phenotype and were used as a disease model to explore the potential of granulocyte-colony stimulating factor in SCA17 treatment. Our results suggest that granulocyte-colony stimulating factor has a neuroprotective effect in these transgenic mice, ameliorating their neurological and behavioral deficits. These data indicate that the expression of the mutant hTBP in Purkinje cells is sufficient to produce cell degeneration and an ataxia phenotype, and constitutes a good model for better analysis of the neurodegeneration in SCA17.

Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles

Emerging fields such as nanomedicine and nanotoxicology, demand new information on the effects of nanoparticles on biological membranes and lipid vesicles are suitable as an experimental model for bio-nano interaction studies. This paper describes image processing algorithms which stitch video sequences into mosaics and recording the shapes of thousands of lipid vesicles, which were used to assess the effect of CoFe(2)O(4) nanoparticles on the population of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine lipid vesicles. The applicability of this methodology for assessing the potential of engineered nanoparticles to affect morphological properties of lipid membranes is discussed.

On the suitability of SIFT technique to deal with image modifications specific to confocal scanning laser microscopy

Computer vision tasks such as recognition and classification of objects and structures or image registration and retrieval can provide significant information when applied to microscopy images. Recently developed techniques for the detection and description of local features make the extraction and description of local image features that are invariant to various changes possible. The invariance and robustness of feature detection and description techniques play a key role in the design and implementation of object recognition, image registration, or image mosaicing applications. The scale-invariant feature transform (SIFT) technique is a widely used method for the detection, description, and matching of image features. In this article we present the results of our experiments regarding the repeatability of SIFT features, and to the precision of the SIFT feature matching, under image modifications specific to confocal scanning laser microscopy (CSLM). We have analyzed the behavior of SIFT while changing the pinhole aperture, photomultiplier gain, laser beam power, and electronic zoom. Our experiments, conducted on CSLM images, show that the SIFT technique is able to match detected key points between images acquired at different values of the acquisition parameters with good precision and represents a consistent tool for computer vision applications in CSLM.

A comparative analysis of constitutive and cell-specific promoters in the adult mouse hippocampus using lentivirus vector-mediated gene transfer

BACKGROUND

Viral vectors provide powerful tools for transgene delivery to the mammalian brain to assess the effects of therapeutic proteins, antisense RNAs or small interfering RNAs. A key advantage of such approaches is that specific brain regions implicated in a particular disease can be independently targeted.

METHODS

To optimize transgene expression in sub-regions of the mouse hippocampus and with a view towards devising gene therapy strategies for Alzheimer's disease, we designed lentivirus-based reporter vectors bearing various promoters, including constitutive and cell-specific promoters. Furthermore, we devised methods allowing a side-by-side comparison of transgene expression levels in neural cells both in vitro and in vivo.

RESULTS

Following stereotaxic injection into the adult mouse hippocampus, titer-adjusted lentiviral vectors bearing constitutive promoters resulted in robust and sub-region-specific transgene expression. Our results show that the human CMV-IE promoter resulted in efficient transgene expression in the entire hippocampus whereas transgene expression mediated by the hybrid hEF1alpha/HTLV promoter was limited mainly in the dentate gyrus and the CA2/3 region. Finally, the neuron-specific human synapsin I promoter was particularly effective in the dentate gyrus.

CONCLUSIONS

These findings indicate that subregion-specific transgene expression in the hippocampus can be achieved following lentivirus vector-mediated gene transfer.

Use of digital video for documentation of microscopic features of tissue samples

CONTEXT

Digital photography is commonly used to document microscopic features of tissue samples, but it relies on the capture of arbitrarily selected representative areas. Current technologic advances permit the review of an entire sample, some even replicating the use of a microscope.

OBJECTIVE

To demonstrate the applicability of digital video to the documentation of histologic samples.

DESIGN

A Canon Elura MC40 digital camcorder was mounted on a microscope, glass slide-mounted tissue sections were filmed, and the unedited movies were transferred to a Apple Mac Pro computer. Movies were edited using the software iMovie HD, including placement of a time counter and a voice recording.

RESULTS

The finished movies can be viewed in computers, incorporated onto DVDs, or placed on a Web site after compression with Flash software. The final movies range, on average, between 2 and 8 minutes, depending on the size of the sample, and between 50 MB and 1.6 GB, depending on the intended means of distribution, with DVDs providing the best image quality.

CONCLUSIONS

Digital video is a practical methodology for documentation of entire tissue samples. We propose an affordable method that uses easily available hardware and software and does not require significant computer knowledge. Pathology education can be enhanced by the implementation of digital video technology.

Electron microscopy of collagen fibril structure in vitro and in vivo including three-dimensional reconstruction

Tissue development in multicellular animals relies on the ability of cells to synthesize an extracellular matrix (ECM) containing spatially organized collagen fibrils, whose length greatly exceeds that of individual cells. The importance of the correct regulation of fibril deposition is exemplified in diseases such as osteogenesis imperfecta (caused by mutations in collagen genes), fibrosis (caused by ectopic accumulation of collagen), and cardiovascular disease (which involves cells and macromolecules binding to collagen in the vessel wall). Much is known about the molecular biology of collagens but less is known about collagen fibril structure and how the fibrils are formed (fibrillogenesis). This is explained in part by the fact that the fibrils are noncrystalline, extensively cross-linked, and very large, which makes them refractory to study by conventional biochemical and high-resolution structure-determination techniques. Electron microscopy has become established as the method of choice for studying collagen fibril structure and assembly. This article describes the electron microscopic methods most often used in studying collagen fibril assembly and structure.

Serial sectioning and three-dimensional reconstruction of mouse Peyer's patch

Peyer's patches (PPs) are typical gut-associated lymphoid tissues that are located along the wall of the small intestine and that serve as the major sites for generation of immunity to intestinal antigens. Their unique micro-organization is crucial for the generation of the immune response. Although many studies have been reported on the functional anatomy of PP, most investigations have relied on the random sampling of these organs, a procedure that is insufficient for the systemic scanning of the whole tissue or organ. By combining a variety of methods, we have accomplished 3D reconstructions of Peyer's patch. The complex reconstruction procedure includes several steps. First, the PP are serially sectioned at a thickness of 10 microm with a cryostat; (b) the serial sections are stained with haematoxylin-eosin; (c) multiple images from the PP are acquired with an automatic microscope and stitched together with Image Pro Plus to generate a composite image for the whole organ; (d) the serial images are reconstructed with Image J, Reconstruct and 3D Studio Max. The combinational approaches that we present here should be of value when extrapolated to the reconstruction of other tissues or organs. Moreover, the 3D model that we have created and our stereological analysis should be extremely helpful for further in vivo microscopic studies of PP with respect to the immune response.