Biofilms are microbial communities developing at the interface between two phases, usually solidliquid, where the micro-organisms are nested in a self-secreted polymer matrix. The biofilm mode of growth is predominant in nature (for e.g. the slimy matter forming on rocks at river bottoms, the viscous deposit in water pipes or even dental plaque) and confers a suitable environment for the development of the micro-organisms. This is particularly the case for porous media which provide favourable substrates given their significant surface to volume ratio. The multi-physical framework of biofilms in porous media is highly complex where the mechanical, chemical and biological aspects interacting at different scales are poorly understood and very partially controlled. An example is the feedback mechanism between flow, spatial distribution of the micro-organisms and the transport of nutrient (by diffusion and advection). Biofilms developing in porous media are a key process of many engineering applications, for example biofilters, soil bio-remediation, CO2 storage and medical issues like infections. Progress in this domain is substantially hindered by the limitations of experimental techniques in metrology and imaging in opaques structures. The main objective of this thesis is to propose robust and reproducible experimental methodologies for the investigation of biofilms in porous media. An experimental workbench under controlled physical and biological conditions is proposed along with a validated 3D imaging protocol based on X-ray micro-tomography (XR MT) using a novel contrast agent (barium sulfate and agarose gel) to quantify the spatial distribution of the biofilm. At first, the XR MT-based methodology is compared to a commonly used techniques for biofilm observation: one or multiple photon excitation fluorescence microscopy, here two-photon laser scanning microscopy (TPLSM). This comparison is performed on Pseudomonas Aeruginosa biofilms grown in transparent glass capillaries which allows for the use of both imaging modalities. Then, the study of uncertainty associated to different metrics namely volume, 3D surface area and thickness, is achieved via an imaging phantom and three different segmentation algorithms. The quantitative analysis show that the protocol enables a visualisation of the biofilm with an uncertainty of approximately 17% which is comparable to TPLSM (14%). The reproducibility and robustness of the XR MT-based methodology is demonstrated. The last step of this work is the achievement of a novel bioreactor elaborated by additive manufacturing and controlled by a high-performance micro-fluidic system. The experimental workbench that we have designed enables to monitor in real-time the evolution of transport properties (effective permeability), O2 concentrations and biofilm detachment by spectrophotometry, all under controlled hydrodynamical conditions. Our methodology allows to investigate the influence of biophysical parameters on the colonisation of the porous medium, for example, the influence of flow rate or nutrient concentration on the temporal development of the biofilm. In conclusion, the thesis work proposes a robust and reproducible experimental methodology for the controlled growth and 3D imaging of biofilms in porous media; while providing versatility in the control of the substrate’s micro-architecture as well as on the flow and biochemical culture conditions. To our knowledge, the scientific approach followed, along with the experimental apparatus, form the most complete methodology, at this time, for the study of biofilms in porous media.

L’imagerie en profondeur in vivo à deux photons est sévèrement limitée par les aberrations optiques. L'optique adaptative est maintenant une technique largement utilisée pour résoudre ce problème. Elle repose sur une des nombreuses techniques possibles de mesure de front d'onde. L'estimation du front d'onde indirecte ou sensorless présente l'avantage d'être facile à mettre en œuvre sur les systèmes existants.L'approche modale sensorless, développée initialement pour l’imagerie à deux photons par Débarre et al., est devenue une technique standard fondée sur la maximisation d'une métrique de qualité d'image telle que l'intensité moyenne de l'image.Cependant, le front d'onde indirectement inféré est influencé par l'échantillon, qui peut induire un biais fort dans l'estimation. Cet effet est connu sous le nom de dépendance en l'échantillon.Ce travail de doctorat vise à développer une approche modale sensorless améliorée qui n'est pas affectée par la dépendance en l'échantillon. J'ai d'abord étudié l'impact des aberrations et de la structure de l'échantillon sur l'intensité moyenne de l'image.Je donne une nouvelle expression analytique de l'intensité moyenne de l'image est donnée qui rend explicite l'interaction entre la forme de la PSF 3D et la distribution spatiale de l'échantillon. À partir de simulations numériques, je montre que la sensibilité de la métrique aux aberrations est préservée pour des échantillons beaucoup plus grands que la résolution spatiale. Deuxièmement, j'étudie l'approche Standard Modal Sensorless (SMS) pour différents types d'échantillons.Je caractérise le problème de la dépendance en l'échantillon induit par des structures très fluorescentes situées hors de la profondeur de focalisation.Ensuite, je montre que la technique displacement-free n’élimine pas complètement la dépendance en l'échantillon.Cette analyse aboutit au développement de notre approche nommée Axially-Locked Modal Sensorless (ALMS). Cette nouvelle approche résout la dépendance en l'échantillon par un réglage automatique et contrôlé de la profondeur de focalisation afin de verrouiller la focalisation sur des motifs brillants de l'échantillon. En outre, l'approche ALMS se fonde également sur une métrique de qualité d'image spécialement conçue pour ce verrouillage. La performance de cette approche est numériquement comparée aux approches SMS et displacement-free. Enfin, ALMS est validée par des tests expérimentaux ex vivo et in vivo. / Deep in vivo two-photon microscopy is severely limited by optical aberrations. Adaptive optics is now a widely used technique to overcome this issue. It relies on one of several possible wavefront sensing techniques. Indirect or sensorless wavefront estimation has the advantage of being easy-to-implement on existing systems. Modal sensorless approach, initially developed for two photon imaging by Débarre et al., has become a standard technique based on the maximization of an image quality metric such as the mean image intensity.However, the indirectly inferred wavefront is influenced by the sample, which may induce a strong bias in the estimation, the so-called sample dependence. This PhD work aims at developing an improved modal sensorless approach that is not affected by sample dependence.I first study the impact of aberrations and of the sample structure on the mean image intensity.A new analytical expression of the mean image intensity is given and makes explicit the interplay between the shape of the 3D PSF and the sample spatial distribution. Through numerical simulations I show that the metric sensitivity to aberrations is preserved for samples much larger than the spatial resolution.Secondly, I study the Standard Modal Sensorless (SMS) approach for different sample scenarios. I characterize the sample dependence issue induced by strong fluorescent structures located out-of-focus. Then, I show that the displacement-free technique fails at fully removing the sample dependence. This analysis leads to the development of our Axially-Locked Modal Sensorless approach (ALMS). This new approach solves the sample dependence by an automatic and controlled adjustment of the focusing depth so as to lock on bright sample features. Furthermore, the ALMS approach is based on a specifically designed image quality metric.The performance of this approach is numerically compared with the SMS and the displacement-free approaches. Finally, ALMS is demonstrated through ex vivo and in vivo experimental tests.

abstract: The OLYMPUS experiment measured the two-photon exchange contribution to elastic electron-proton scattering, over a range of four-momentum transfer from \(0.6 < Q^2 < 2.2\) \((\mathrm{GeV/c})^2\). The motivation for the experiment stemmed from measurements of the electric-to-magnetic form factor ratio of the proton \(\mu G_E/G_M\) extracted from polarization observables in polarized electron-proton scattering. Polarized electron-proton scattering experiments have revealed a significant decrease in \(\mu G_E/G_M\) at large \(Q^2\), in contrast to previous measurements from unpolarized electron-proton scattering. The commonly accepted hypothesis is that the discrepancy in the form factor ratio is due to neglected higher-order terms in the elastic electron-proton scattering cross section, in particular the two-photon exchange amplitude. The goal of OLYMPUS was to measure the two-photon exchange contribution by measuring the positron-proton to electron-proton elastic scattering cross section ratio, \(\sigma_{e^+p}/\sigma_{e^-p}\). The two-photon exchange contribution is correlated to the deviation of the cross section ratio from unity. In 2012, the OLYMPUS experiment collected over 4 fb\(^{-1}\) of \(e^+p\) and \(e^-p\) scattering data using electron and positron beams incident on a hydrogen gas target. The scattered leptons and protons were measured exclusively with a large acceptance spectrometer. OLYMPUS observed a slight rise in \(\sigma_{e^+p}/\sigma_{e^-p}\) of at most 1-2\% over a \(Q^2\) range of \(0.6 < Q^2 < 2.2\) \((\mathrm{GeV/c})^2\). This work discusses the motivations, experiment, analysis method, and the preliminary results for the cross section ratio as measured by OLYMPUS. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

Bacillus anthracis, l'agent infectieux responsable de la maladie du charbon, est un agent pathogène majeur du risque biologique provoqué, notamment en raison de la sévérité de la forme respiratoire de la maladie. Celle-ci résulte de l'inhalation de spores dont les mécanismes de pénétration au niveau pulmonaire sont mal connus à l'heure actuelle. Cette thèse présente les apports des microscopies confocale et biphotonique à l'étude de ces mécanismes de pénétration des spores inhalées. Le modèle murin CX3CR1+/gfp, dont la sous-population CD11b+ de cellules dendritiques (DCs) exprime constitutivement la protéine de fluorescence verte (GFP), a été utilisé dans ces travaux. Une première partie présente le développement d'une méthode automatisée de discrimination des DCs parmi d'autres populations cellulaires exprimant le même fluorophore, en se basant sur le calcul d'un coefficient morphologique. Cette méthode a permis d'étudier dans un deuxième temps le comportement spécifique de la sous-population de DCs CD11b, après infection par des spores de B. anthracis. L'étude microscopique a été d'abord effectuée in situ, c'est-à-dire sur des explants pulmonaires maintenus dans des conditions favorables à la préservation de l'activité cellulaire, puis in vivo, sur des souris anesthésiées et ventilées. Le protocole d'imagerie tire profit d'une stratégie d'acquisition et de traitement a posteriori des données permettant de surmonter, sans contrainte mécanique appliquée à l'organe, les problèmes de focalisation liés aux mouvements thoraciques durant la ventilation de l'animal. Cette stratégie originale utilise un sur-échantillonnage de l'acquisition et profite du signal de seconde harmonique généré par le collagène comme référence spatiale ; elle a permis l'observation in vivo d'interactions entre DCs et macrophages au niveau pulmonaire. Ces interactions, de type synapse immunologique, sont favorisées par l'infection et présentent donc un rôle fonctionnel qui reste à définir. La formation de synapses immunologiques entre macrophages et DCs pourrait non seulement représenter un chaînon manquant à l'explication de la pénétration des spores de B. anthracis au niveau pulmonaire, mais pourrait aussi constituer un enjeu crucial dans la compréhension de la réponse immunitaire associée aux infections pulmonaires. / Bacillus anthracis, the causative agent of anthrax, is a major bioterrorism pathogen mainly because it can lead to a severe respiratory form of the disease. This form results from inhalation of spores, whose ways of entry into the lungs are not fully understood. This thesis reports the contribution of confocal and two-photon microscopy to the study of the penetration mechanisms of inhaled spores. The animal model utilized was CX3CR1+/gfp mouse, which constitutively expresses the green fluorescent protein (GFP) on CD11b+ dendritic cells (DCs). First, we present an automated method allowing discrimination of DCs among other GFP expressing cells, based on a morphologic coefficient. This method was then applied to the study of the specific behavior of CD11b DCs, after infection by B. anthracis spores. The microscopic study was first performed in situ, i.e. on explanted organs kept in conditions favorable to cell dynamics, then in vivo, i.e. on anesthetized and ventilated mice. In this case the imaging protocol profits from both acquisition and post-processing strategies, and allowed overcoming the focalization pitfalls coming from chest movements during ventilation. This novel strategy is based on an over-sampling of frame acquisition and utilizes second harmonic generation signal from alveolar collagen as a spatial reference. It led to the first ever in vivo observation of interactions between DCs and macrophages at the lung level. These immunological synapse-like structures are promoted by infection and thus display a functional role unknown until now. The formation of macrophages-DCs immunological synapses not only could represent a missing-link in figuring out the B. anthracis spore penetration mechanisms at the lung level, but more importantly could lead to a better understanding of the immune response associated with pulmonary infections.

Neste trabalho estudamos o processo de absorção de dois fótons em compostos azoaromáticos, abordando tanto aspectos fundamentais quanto aplicados. Moléculas azo-aromáticos têm recebido especial atenção nos últimos anos devido as suas potencias aplicações em dispositivos para armazenamento óptico de informação, modulação da luz e geração de relevos em superfície, processes estes associados ao mecanismo de foto isomerização. Os trabalhos apresentados nessa tese tiveram como principal foco explorar o fenômeno de absorção de dois fótons, utilizando a propriedade de foto-isomerização das moléculas azo-aromáticas. Nosso objetivo foi estudar as vantagens que podem ser obtidas pela utilização de pulsos intensos de luz, que interagem de maneira não linear com a matéria, para desenvolver aplicações utilizando compostos azo-aromáticos. Inicialmente, estudamos o processo de absorção de dois fótons em uma nova família de compostos azo-aromáticos, denominados Salen Dyes. Investigamos a influencia da presença de íons metálicos no processo de absorção de dois fótons dessas moléculas. Nossos resultados mostraram que, devido a ausência de conjugação entre as estruturas azo-aromáticas conectadas pelo metal, este tem pouca influência no processo não linear estudado. Pelo uso de um modelo de soma de estado para a seção de choque de absorção de dois fótons, fomos capazes de determinar os momentos de dipolo de transição destas moléculas. Em seguida, implementamos uma técnica para estudar o processo de armazenamento óptico, induzido através da orientação molecular dos compostos azo-aromáticos, via absorção de dois fótons. Observamos que de fato é possível se observar birrefringência induzida por dois fótons nestas moléculas, a qual esta confinada ao volume focal, conforme demonstrado pela obtenção de armazenamento tri-dimensional. Finalmente, exploramos o processo de controle coerente via formatação de pulsos ultra-curtos para manipular o processo de birrefringência induzida por dois fótons em compostos azo-aromáticos. Foi demonstrado que apenas a através da manipulação da fase do pulso ultra-curto, é possível modular a birrefringência induzida em filmes de compostos azo-aromáticos. / Here we investigated fundamental and applied aspects of the two-photon absorption process in azoaromatic compounds. Azoaromatic molecules have been studied in the last few years due to their applications in optical storage devices, light modulators and surface relief gratings, processes related to the photo-isomerization mechanism. The main focus of the results presented in this thesis was to explore the two-photon absorption process, taking advantage of the intrinsic photo-isomerization of the azo-aromatic chromophores. Our main goal was to study the advantages of utilizing intense pulses, which promote nonlinear excitation, to develop application with azo-aromatic compounds. Initially, we studied the two-photon absorption process in a new class of azo-aromatic compounds, named Salen Dyes. We investigated the influence of metal ions, presented in the Salen Dyes structure, on the two-photon absorption spectrum. Our results revealed that the metals have practically no influence in the nonlinear optical properties due to the lack of conjugation between the azo-moieties in the Salen Dyes. Through a theoretical model based on a sum-over-states calculation, we were able to determine the transition dipole moment of these molecules. Subsquently, we implememnted a technique to study the two-photon induced birefringence, resulting from the molecular re-orientation, in azo-aromatic compounds. We observed that the two-photon induced birefringence is confined to the focal volume, s demonstrated in a three dimensional optical storage experiment. Finally, we used coherent control processes to manipulate the two-photon induced birefringence in azo-compounds. It was demonstrated that it is possible to modulate the optically induced birefringence by manipulating the phase of the ultra-short pulses, via pulse shaping techniques.

Neste trabalho estudamos a forma de linha na absorção de dois fotons nas transições 4f7 de defeitos cristalinos superpostas com bandas de absorção multifonons. Escrevemos o perfil de linha sob a forma de Fano. O íon em estudo é Eu++ como defeito em um cristal de CaF2. Apresentamos o desenvolvimento da instrumentação necessária para realização do experimento, e obtemos resultados de ótima qualidade. / In this work we study the absorption of two photons in the electronic transition within the 4f 7configuration wich is superposed to the vibronic structure of 4f 7 - 4f65d transition. We describe the line shape with the Fano\'s formalism. The study was carried out on Eu+2 doped CaF2. The experimental apparatus was build and the results obtained are in good agreement with the theoretical predictions.

Neste trabalho estudamos a absorção cooperativa de dois fótons em processos de colisão entre átomos frios de sódio aprisionados. Efeitos não-lineares exigem amostras de alta densidade para ser observados. Redesenhamos nosso sistema experimental para conseguir amostras de 1012 átomos/cm3. As principais alterações foram a construção de um desacelerador Zeeman em configuração spin-flip, a implementação de bombeamento diferencial entre o forno e a câmara principal, assim como redesenhar o forno. A fim de compreender e melhorar os processos de medição utilizamos a técnica de fotoionização nos estados 32P1/2 e 32P3/2. Com esses dados conseguimos calcular a seção transversal de ionização para cada um desses estados, que está de acordo com valores reportados na literatura. Estes resultados mostram que o novo desenho do sistema permite um grande ponto de partida para a medição da absorção de dois fótons. Uma tentativa de medir a absorção de dois fótons foi feita. Um pequeno aumento no número de íons produzidos por unidade de tempo foi observada em uma região deslocada para o vermelho de cerca de 4,5 GHz de onde inicialmente se esperava ocorrer a transição. Isto motiva a aprofundar o estudo da absorção de dois fótons, já que provavelmente essa medida seja um indício da ocorrência desse fenômeno. Assim, tanto a medição da seção de choque dos estados 32P1/2 e 32P3/2 e a tentativa de medir a absorção de dois fótons, fornecem uma base sólida para conhecer qual é a melhor maneira de obter resultados mais decisivos no que diz respeito à absorção cooperativa de dois fótons, e as vantagens do nosso sistema em futuros experimentos. / In this work we study the cooperative two-photon absorption in collisional processes between cold trapped sodium atoms. Nonlinear effects require high density samples to be observed. We redesign our experimental system to achieve samples up to 1012 atoms/ cm3 .The key changes were building a spin-flip Zeeman slower, implementing differential pumping between the oven and the chamber and changing the oven´s design. In order to understand and improve the measurement processes we did photoionization from the states 32P1/2 e 32P3/2. With this data we could calculate the ionization cross section for each of these states, which is in agreement with values reported in the literature. These results show that the new design of the system allows a great starting point for measuring of two-photon absorption. An attempt to measure the absorption of two-photon was made. A small increase in the number of ions produced per unit time was observed in a region shifted to the red of about 4.5 GHz from where we initially expected the transition to occur. This probably indicates two-photon absorption. Thus, both the measurement of cross section of states and the attempt to measure the absorption of two photons, provide a solid foundation for understanding what is the best way to obtain more decisive results with regard to cooperative absorption, and the advantages of performance of our system in future experiments.

Neste trabalho apresentamos resultados de birrefringência opticamente induzida via absorção de um e dois fótons em filmes casting de poli (metil metacrilato) (PMMA), contendo uma nova série de compostos azoaromáticos chamados de corantes Salen, os quais podem ser usados em aplicações de memória óptica. Para a birrefringência opticamente induzida por um fóton, foi necessário um tempo de escrita maior para os compostos com metal na estrutura em comparação com o composto Salen que não contém metal, provavelmente devido a agregações do grupo azoaromático na estrutura do polímero diminuindo a mobilidade molecular. Além disso, como uma novidade em memórias ópticas deste tipo, birrefringência opticamente induzida por dois fótons pôde ser realizada nos filmes de Salen, o que pode permitir sua aplicação em memória óptica tridimensional. / In this work we present the one- and two-photon optically induced birefringence in cast films of amorphous poly(methyl methacrylate) (PMMA), containing a new series of organometallic azoaromatic compounds, referred to as Salen dyes, which may be used in optical storage applications. For the one-photon optically induced birefringence, longer writing times were required for the organometallic compounds in comparison with the nonmetal one, probably due to the higher degree of aggregation in the azoaromatic moieties that precludes molecular orientation. Furthermore, as a novelty concerning optical storage, two-photon optically induced birefringence could be achieved in the Salen dyes guest-host films, which allows their application in three-dimensional optical memories.

Neste trabalho estudamos através de técnicas de espectroscopia de dois fótons, transições entre níveis de um defeito de configuração 4f7, transições estas proibidas via um único fóton. Analisamos o efeito do campo cristalino sob os níveis de energia do defeito. O íon estudado foi o Eu+2 com defeito nas matrizes de CaF2, KCl, KI. Desenvolvemos alguns equipamentos e instrumentos necessários para realização do experimento. Os espectros de absorção de dois fótons nas transições 4f7(8S7/2) &#8594 4f7 (8P7/2) apresentam-se como um conjunto de três e quatro linhas estreitas nas simetrias Oh e C2v respectivamente. Estes resultados estão em concordância com os cálculos de teoria de grupo. As transições 4f7(8S7/2) &#8594 4f7 (8P5/2) apresentam-se como duas linhas na simetria Oh (CaF2) em concordância com os cálculos teóricos. No caso dos cristais com simetria C2v essas transições são inexplicavelmente ausentes. / We have applied the technique of two photon absorption to study transitions between different levels of the 4f7 configuration. These transitions are forbidden for one photon. The effect of the crystal field in these electronic states is studied. The ion we have chosen is Eu+2 in ionic crystals of KCl, KI and CaF2. The experimental technique was implanted at the laboratory with several parts developed by ourselves. The two photon absorption spectra of the 4f7(8S7/2) &#8594 4f7 (8P7/2) is composed of three and four sharp lines in the Oh and C2v symmetry respectively. These results are in agreement with the group theory calculations of the problem. The transition 4f7(8S7/2) &#8594 4f7 (8P5/2) appears as two sharp lines in the Oh symmetry (CaF2) in agreement with the theory, those transitions are not present in the crystals with C2v symmetry and this result is not understood.

Neste trabalho, demonstramos a fabricação de microambientes tridimensionais para investigar o crescimento celular. Inicialmente, desenvolvemos um sistema de microfabricação que utiliza fotopolimerização via absorção de dois fótons, com o qual se pode fabricar um conjunto de microestruturas com formas e espaçamentos pré-determinados. Este sistema de fabricação utiliza pulsos de femtossegundos, provenientes de um laser de Ti:safira operando em 790 nm. A intensidade destes pulsos é alta o bastante para induzir a absorção de dois fótons no fotoiniciador, o qual é responsável por promover a polimerização em uma resina acrílica. A natureza não linear da absorção de dois fótons confina a excitação ao volume focal, permitindo a fabricação de estruturas tridimensionais com alta resolução espacial. Para a obtenção dos microambientes, foi necessário o desenvolvimento de um sistema opto-mecânico de movimentação, tanto do feixe quando do substrato da amostra. Com esta técnica, fabricamos microambientes compostos de estruturas com diferentes formas (paralelepípedos, cilindros e cones) e espaçamentos, os quais foram caracterizados através de microscopia óptica e eletrônica. Para demonstrar a viabilidade destes microambientes para a investigação do crescimento celular, estes foram utilizados para monitorar o desenvolvimento da célula Michigan Cancer Foundation-7 (MCF-7), uma linhagem celular de adenocarcinoma de mama que apresenta fenótipo tumoral amplamente utilizada como modelo de estudo para câncer de mama. Observamos, via microscopia óptica de transmissão e fluorescência, o desenvolvimento das células MCF-7 nos distintos microambientes. Nossos resultados indicam uma melhor aderência e, portanto, desenvolvimento celular nas microestruturas cilíndricas. Observamos ainda uma maior densidade de células nos microambientes com estruturas separadas de 12 &micro;m, a qual diminui com o aumento do espaçamento, de tal forma que para o microambiente com 30 &micro;m, por exemplo, poucas células são observadas. Portanto, nossos resultados demonstram que os microambientes desenvolvidos são viáveis para estudos mais aprofundados em biologia celular, com potenciais aplicações em engenharia de tecido. / In this work we have demonstrated the fabrication of tridimensional microenvironments for the investigation of cell growth. Initially we have developed a two-photon absorption photopolymerization microfabrication system, which allows producing a set of microstructures with predetermined forms and spacing. This fabrication system uses femtosecond pulses from a Ti: sapphire laser operating at 790 nm. These pulses are intense enough to induce two-photon absorption by the photoinitiator, that is responsible for promoting the polymerization in an acrylic resin. The nonlinear nature of the two-photon absorption confines the excitation to the focal volume, allowing the fabrication of tridimensional structures with high spatial resolution. In order to obtain the microenvironments, it was necessary to develop a movement system for both the laser beam and the sample substrate. With this technique we have fabricated microenvironments composed by structures with different geometries (parallelepipeds, cylinders and cones) and spacing, which were characterized by optical and scanning electron microscopes. To demonstrate the feasibility of the microenvironments for the investigation of cell growth, the samples were used to monitor de development of the Michigan Cancer Foundation-7 cell (MCF-7), a lineage of breast adenocarcinoma that has a tumoral phenotype and is highly used as a model in breast cancer studies. We have observed, through conventional optical and fluorescence microscopy, the growth of the MCF-7 cells in the various microenvironments. Our results indicate a better adhesion and, therefore, better development of cells on the cylindrical microstructures. We also observe a higher cell density in the microenvironments with microstructures having a spacing of 12 &micro;m, which reduces as the distance between microstructures increases, in such a way that for the microenvironment with 30 &micro;m spacing, for example, just a few cells are observed. Thus, our results demonstrate that the produced microenvironments are applicable in deeper studies in microbiology, with potential application in tissue engineering.