Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

[0 0 1] zone-axis bright-field diffraction contrast from coherent Ge(Si) islands on Si(0 0 1): Dedicated to Professor Fang-hua Li on the occasion of her 70th birthday

Coherent Ge(Si)/Si(001) quantum dot islands grown by solid source molecular beam epitaxy at a growth temperature of 700degreesC were investigated using transmission electron microscopy working at 300 kV. The [001] zone-axis bright-field diffraction contrast images of the islands show strong periodicity with the change of the TEM sample substrate thickness and the period is equal to the effective extinction distance of the transmitted beam. Simulated images based on finite element models of the displacement field and using multi-beam dynamical diffraction theory show a high degree of agreement. Studies for a range of electron energies show the power of the technique for investigating composition segregation in quantum dot islands. (C) 2003 Elsevier B.V. All rights reserved.

Multiple excitation nano-spot generation and confocal detection for far-field microscopy

An imaging technique is developed for the controlled generation of multiple excitation nano-spots for far-field microscopy. The system point spread function (PSF) is obtained by interfering two counter-propagating extended depth-of-focus PSF (DoF-PSF), resulting in highly localized multiple excitation spots along the optical axis. The technique permits (1) simultaneous excitation of multiple planes in the specimen; (2) control of the number of spots by confocal detection; and (3) overcoming the point-by-point based excitation. Fluorescence detection from the excitation spots can be efficiently achieved by Z-scanning the detector/pinhole assembly. The technique complements most of the bioimaging techniques and may find potential application in high resolution fluorescence microscopy and nanoscale imaging.

Automatic segmentation and classification of human intestinal parasites from microscopy images

Human intestinal parasites constitute a problem in most tropical countries, causing death or physical and mental disorders. Their diagnosis usually relies on the visual analysis of microscopy images, with error rates that may range from moderate to high. The problem has been addressed via computational image analysis, but only for a few species and images free of fecal impurities. In routine, fecal impurities are a real challenge for automatic image analysis. We have circumvented this problem by a method that can segment and classify, from bright field microscopy images with fecal impurities, the 15 most common species of protozoan cysts, helminth eggs, and larvae in Brazil. Our approach exploits ellipse matching and image foresting transform for image segmentation, multiple object descriptors and their optimum combination by genetic programming for object representation, and the optimum-path forest classifier for object recognition. The results indicate that our method is a promising approach toward the fully automation of the enteroparasitosis diagnosis. © 2012 IEEE.

Oocyte meiotic-stage-specific differences in spindle depolymerization in response to temperature changes monitored with polarized field microscopy and immunocytochemistry

Objective: To compare the polymerization status of mouse oocyte spindles exposed to various temperatures at various stages of meiosis. Design: Experimental animal study. Setting: University animal laboratory. Animal(s): CF1 mice. Intervention(s): Immature oocytes matured to metaphase I (MI), telophase I (TI), and metaphase II (MII) were incubated at 37 degrees C (control), room temperature (RT), or 4 degrees C for 0, 10, 30, and 60 minutes. Spindle analysis subsequently was performed using polarized field microscopy and immunocytochemistry. Spindles of TI and MII oocytes that underwent vitrification and warming were analyzed also by immunocytochemistry. Main Outcome Measure(s): Detection of polymerized meiotic spindles. Result(s): At RT, and after 60 minutes at 4 degrees C, a significant time-dependent decrease in the percentage of polymerized meiotic spindles was observed in MI and MII oocytes, but not in TI oocytes. The polymerization of TI spindles at 4 degrees C was similar to that of TI spindles at 4 degrees C that underwent vitrification and warming. Conclusion(s): Significant differences in the microtubule dynamics of MI, TI, and MII oocytes incubated at different temperatures were observed. In particular, meiotic spindles in TI oocytes exhibited less depolymerization than did metaphase spindles. (Fertil Steril (R) 2012; 97: 714-9. (C) 2012 by American Society for Reproductive Medicine.)

Towards a precise test for malaria diagnosis in the Brazilian Amazon: comparison among field microscopy, a rapid diagnostic test, nested PCR, and a computational expert system based on artificial neural networks

Abstract Background Accurate malaria diagnosis is mandatory for the treatment and management of severe cases. Moreover, individuals with asymptomatic malaria are not usually screened by health care facilities, which further complicates disease control efforts. The present study compared the performances of a malaria rapid diagnosis test (RDT), the thick blood smear method and nested PCR for the diagnosis of symptomatic malaria in the Brazilian Amazon. In addition, an innovative computational approach was tested for the diagnosis of asymptomatic malaria. Methods The study was divided in two parts. For the first part, passive case detection was performed in 311 individuals with malaria-related symptoms from a recently urbanized community in the Brazilian Amazon. A cross-sectional investigation compared the diagnostic performance of the RDT Optimal-IT, nested PCR and light microscopy. The second part of the study involved active case detection of asymptomatic malaria in 380 individuals from riverine communities in Rondônia, Brazil. The performances of microscopy, nested PCR and an expert computational system based on artificial neural networks (MalDANN) using epidemiological data were compared. Results Nested PCR was shown to be the gold standard for diagnosis of both symptomatic and asymptomatic malaria because it detected the major number of cases and presented the maximum specificity. Surprisingly, the RDT was superior to microscopy in the diagnosis of cases with low parasitaemia. Nevertheless, RDT could not discriminate the Plasmodium species in 12 cases of mixed infections (Plasmodium vivax + Plasmodium falciparum). Moreover, the microscopy presented low performance in the detection of asymptomatic cases (61.25% of correct diagnoses). The MalDANN system using epidemiological data was worse that the light microscopy (56% of correct diagnoses). However, when information regarding plasma levels of interleukin-10 and interferon-gamma were inputted, the MalDANN performance sensibly increased (80% correct diagnoses). Conclusions An RDT for malaria diagnosis may find a promising use in the Brazilian Amazon integrating a rational diagnostic approach. Despite the low performance of the MalDANN test using solely epidemiological data, an approach based on neural networks may be feasible in cases where simpler methods for discriminating individuals below and above threshold cytokine levels are available.

Características morfológicas de vermes adultos de Schistosoma mansoni Sambon, 1907 recuperados de camundongos alimentados com dieta hiperlípidíca na fase crônica da infecção esquistossomótica. Análise por microscopia de campo claro e confocal

Estudos em animais experimentais evidenciaram associações significativas entre esquistossomose mansoni e hipercolesterolemia. Estudos in vitro e in vivo já demonstraram que o colesterol é essencial para Schistosoma mansoni, embora este não tenha capacidade de sintetizá-lo. A captação é realizada a partir do ambiente (cultivo ou hospedeiro) através do tegumento. O colesterol está envolvido nos mecanismos de evasão do helminto contra a resposta imunológica, além de poder participar na modulação da sinalização celular e reprodução, estimulando os órgãos reprodutores dos helmintos adultos como observado na fase aguda da infecção experimental. Este trabalho tem como objetivo avaliar se o mesmo fenômeno ocorre na fase crônica. Os helmintos foram recuperados de dez camundongos submetidos à dieta hiperlipídica ou padrão (controle) foram corados pelo carmin cloridrico e montados, individualmente, em lâmina histológica com bálsamo do Canadá. A preparação foi analisada por microscopia de campo claro nos seguintes caracteres: tegumento e o sistema reprodutor nos vermes machos (lobos testiculares, vesícula seminal, lobos testiculares supranumerários e canal ginecóforo) e, nas fêmeas (ovário, oótipo, útero, ovo, glândulas vitelínicas e espermateca). Posteriormente, algumas lâminas foram separadas para visualização pela microscopia confocal dos órgãos do sistema reprodutores acima descritos. Apesar de ter sido observado uma maior quantidade de espermatozoides, uma maior quantidade de oócitos sendo liberados no grupo da dieta, não houve diferença estatística significativa (p>0,05) entre os grupos analisados. Houve um aumento na oogênese como observado na fase aguda. Dessa forma, o colesterol pode estar relacionado com a estimulação na atividade dos órgãos reprodutores dos helmintos adultos na fase crônica da infecção.

Cultivo de Eucalyptus urograndis em atmosfera enriquecida com CO2: mudanças no proteoma cloroplastidial

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Développement et caractérisation d’une méthode photonique pour créer des distributions spatiales de protéines

Les cellules sont capables de détecter les distributions spatiales de protéines et ainsi de migrer ou s’étendre dans la direction appropriée. Une compréhension de la réponse cellulaire aux modifications de ces distributions spatiales de protéines est essentielle pour l’avancement des connaissances dans plusieurs domaines de recherches tels que le développement, l’immunologie ou l’oncologie. Un exemple particulièrement complexe est le guidage d’axones se déroulant pendant le développement du système nerveux. Ce dernier nécessite la présence de plusieurs distributions de molécules de guidages étant attractives ou répulsives pour connecter correctement ce réseau complexe qu’est le système nerveux. Puisque plusieurs indices de guidage collaborent, il est particulièrement difficile d’identifier la contribution individuelle ou la voie de signalisation qui est déclenchée in vivo, il est donc nécessaire d’utiliser des méthodes pour reproduire ces distributions de protéines in vitro. Plusieurs méthodes existent pour produire des gradients de protéines solubles ou liées aux substrats. Quelques méthodes pour produire des gradients solubles sont déjà couramment utilisées dans plusieurs laboratoires, mais elles limitent l’étude aux distributions de protéines qui sont normalement sécrétées in vivo. Les méthodes permettant de produire des distributions liées au substrat sont particulièrement complexes, ce qui restreint leur utilisation à quelques laboratoires. Premièrement, nous présentons une méthode simple qui exploite le photoblanchiment de molécules fluorescentes pour créer des motifs de protéines liées au substrat : Laser-assisted protein adsorption by photobleaching (LAPAP). Cette méthode permet de produire des motifs de protéines complexes d’une résolution micrométrique et d’une grande portée dynamique. Une caractérisation de la technique a été faite et en tant que preuve de fonctionnalité, des axones de neurones du ganglion spinal ont été guidés sur des gradients d’un peptide provenant de la laminine. Deuxièmement, LAPAP a été amélioré de manière à pouvoir fabriquer des motifs avec plusieurs composantes grâce à l’utilisation de lasers à différentes longueurs d’onde et d’anticorps conjugués à des fluorophores correspondants à ces longueurs d’onde. De plus, pour accélérer et simplifier le processus de fabrication, nous avons développé LAPAP à illumination à champ large qui utilise un modulateur spatial de lumière, une diode électroluminescente et un microscope standard pour imprimer directement un motif de protéines. Cette méthode est particulièrement simple comparativement à la version originale de LAPAP puisqu’elle n’implique pas le contrôle de la puissance laser et de platines motorisées, mais seulement d’envoyer l’image du motif désiré au modulateur spatial. Finalement, nous avons utilisé LAPAP pour démontrer que notre technique peut être utilisée dans des analyses de haut contenu pour quantifier les changements morphologiques résultant de la croissance neuronale sur des gradients de protéines de guidage. Nous avons produit des milliers de gradients de laminin-1 ayant différentes pentes et analysé les variations au niveau du guidage de neurites provenant d’une lignée cellulaire neuronale (RGC-5). Un algorithme pour analyser les images des cellules sur les gradients a été développé pour détecter chaque cellule et quantifier la position du centroïde du soma ainsi que les angles d’initiation, final et de braquage de chaque neurite. Ces données ont démontré que les gradients de laminine influencent l’angle d’initiation des neurites des RGC-5, mais n’influencent pas leur braquage. Nous croyons que les résultats présentés dans cette thèse faciliteront l’utilisation de motifs de protéines liées au substrat dans les laboratoires des sciences de la vie, puisque LAPAP peut être effectué à l’aide d’un microscope confocal ou d’un microscope standard légèrement modifié. Cela pourrait contribuer à l’augmentation du nombre de laboratoires travaillant sur le guidage avec des gradients liés au substrat afin d’atteindre la masse critique nécessaire à des percées majeures en neuroscience.

Natural latex graft in lamellar and penetrating sclerectomies in rabbits

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Cultivo de Eucalyptus urograndis em atmosfera enriquecida com CO2: mudanças no proteoma cloroplastidial

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Systemically alendronate was incorporated into dental tissues but did not cause morphological or mechanical changes in rats teeth

This study evaluated the effect of the systemic use of sodium alendronate in rats in vivo. Forty-five Wistar rats aged 36 to 42 days and weighing 200 to 230 g were randomly assigned to a control group (n = 20), which received distilled water, and an experimental group (n = 25), which received 2 weekly doses of 1 mg/kg of chemically pure sodium alendronate. The animals were killed after 60 days of treatment. The tibias were removed for analysis of bone mineral density by dual-energy X-ray absorptiometry (DXA). Then, the maxillary incisors were extracted for analysis of the mineralized dental tissues using fluorescence spectroscopy (FS), scanning electron microscopy (SEM), bright field microscopy (BFM), and cross-sectional microhardness (CSMH) testing. DXA and CSMH data were subjected to statistical analysis by Kruskal-Wallis test (5% significance level). The experimental group presented higher bone mineral density than the control group by DXA. FS analysis revealed presence of alendronate in the mineralized dental tissues of the specimens of the experimental group. Significant morphological differences were not found by SEM and BFM. Enamel and dentin (100 and 300 mu m from the dentinoenamel junction) CSMH data did not show significant difference between the control and experimental groups. Based on the obtained results, we conclude that while alendronate increased the bone mineral density and was incorporated into the mineralized dental tissues it did not cause significant alterations in the morphology and microhardness of rat incisor enamel and dentin. Microsc. Res. Tech. 75:12651271, 2012. (C) 2012 Wiley Periodicals, Inc.

Dipsacus asperoides (Xue Duan) inhibits spinal cord injury-induced inflammatory responses in rats

Purpose: To investigate the effect of Dipsacus asperoides (Xue Duan), a traditional Chinese medicine, on rats with spinal cord injury (SCI). Methods: In this study a total of 40 adult rats were used after inducing SCI where Xue Duan was applied on experimental group and phosphate-buffered saline (PBS) was administered in corresponding control groups. Intraperitoneal administration of both compounds for a period of four weeks (28 days) was carried out at a dose of 10 mg/kg/day. Bright field microscopy was performed on the tissues. Results: Bright Field microscopy of tissue sections showed significant reduction in cavity area that resulted from injury, that is from 0.19 ± 0.05 mm2 to 0.09 ± 0.03 mm2 (p < 0.01) in untreated and treated groups respectively. Similarly western blotting results showed a decrease in the expression of NF-kB p65 and I-kBα (p < 0.01). These two compounds are important in increasing secondary pathophysiology in SCI. The results for MPO activity also revealed significantly reduced infiltration of leukocytes to the injury site (p < 0.01). Conclusion: This study reveals the positive effect of the plant material in reducing inflammation in rats with traumatic SCI.