DeadEasy Mito-Glia: Automatic Counting of Mitotic Cells and Glial Cells in Drosophila

Cell number changes during normal development, and in disease (e.g., neurodegeneration, cancer). Many genes affect cell number, thus functional genetic analysis frequently requires analysis of cell number alterations upon loss of function mutations or in gain of function experiments. Drosophila is a most powerful model organism to investigate the function of genes involved in development or disease in vivo. Image processing and pattern recognition techniques can be used to extract information from microscopy images to quantify automatically distinct cellular features, but these methods are still not very extended in this model organism. Thus cellular quantification is often carried out manually, which is laborious, tedious, error prone or humanly unfeasible. Here, we present DeadEasy Mito-Glia, an image processing method to count automatically the number of mitotic cells labelled with anti-phospho-histone H3 and of glial cells labelled with anti-Repo in Drosophila embryos. This programme belongs to the DeadEasy suite of which we have previously developed versions to count apoptotic cells and neuronal nuclei. Having separate programmes is paramount for accuracy. DeadEasy Mito-Glia is very easy to use, fast, objective and very accurate when counting dividing cells and glial cells labelled with a nuclear marker. Although this method has been validated for Drosophila embryos, we provide an interactive window for biologists to easily extend its application to other nuclear markers and other sample types. DeadEasy MitoGlia is freely available as an ImageJ plug-in, it increases the repertoire of tools for in vivo genetic analysis, and it will be of interest to a broad community of developmental, cancer and neuro-biologists

Cytokinesis in the mouse preimplantation embryo : mechanism and consequence of failure

Essentiel au maintien d’un organisme sain, la division cellulaire est un processus biologique composée de deux phases : la mitose et la cytokinèse. Au cours de la mitose, un fuseau mitotique bipolaire est assemblé et les chromosomes s’alignent au niveau de la plaque métaphasique par l’attachement des kinétochores aux microtubules du fuseau. Une fois les chromosomes alignés, les chromatides soeurs sont séparées par les microtubules pendant l'anaphase et sont ségréguées entre les cellules filles. La cytokinèse est initiée peu après le début de l'anaphase, marquant ainsi la fin de la division cellulaire en séparant le cytoplasme en deux nouvelles cellules filles. Une exécution précise de la mitose et de la cytokinèse est essentielle pour le maintien de l'intégrité du génome. L'échec de l'un de ces processus affecte la fidélité génétique. Les erreurs de ségrégation des chromosomes durant la mitose peuvent entraîner un gain ou une perte de chromosomes entiers, appelé aneuploïdie. Tandis que l'échec de la cytokinèse conduit à la formation d'une cellule binucléée avec un génome entièrement dupliqué, appelé tétraploïdie. Dans les cellules somatiques, la tétraploïdie peut conduire à l'arrêt du cycle cellulaire, à la mort cellulaire, ou provoquer une instabilité chromosomique (CIN), favorisant ainsi la prolifération de cellules avec un potentiel tumorigène. Par conséquent, il est essentiel de bien comprendre la régulation et les causes potentielles de l’échec de la cytokinèse en particulier dans le contexte des systèmes multicellulaires comme l’embryon. En effet, dans ces systèmes, la réduction progressives de la taille des cellules coïncident avec les principaux évènements du développement. De plus, la binucléation est fréquemment observée dans les cliniques de fertilité chez les embryons humains. Cependant, l’impact de la binucléation sur les divisions préimplantatoires demeure inexpliqué à ce jour. Afin de déterminer les conséquences de la tétraploïdie, nous avons utilisé l'embryon de souris pour modèle et réalisé des expériences d'immunofluorescence à haute résolution et une imagerie sur cellules vivantes. Nous avons découvert que la tétraploïdie chez les embryons de souris provoque une CIN et l'aneuploïdie par un mécanisme différent de celui des cellules somatiques. Dans les cellules somatiques, la formation des fuseaux multipolaires causée par des centrosomes surnuméraires est le principal mécanisme conduisant à la tétraploïdie et ainsi, à une CIN. En revanche, chez les embryons de souris, qui ne possèdent pas de centrosomes, la tétraploïdie ne conduit pas à la formation des fuseaux multipolaires. Les embryons tétraploïdes de souris développent une CIN en raison d’une réduction du renouvellement des microtubules et d’une altération de l’activité de correction d’erreurs dans l’attachement des kinétochores aux microtubules. Ainsi, une mauvaise correction de l’attachement des kinétochores aux microtubules entraîne des niveaux élevés d'erreurs de ségrégation chromosomique. Dans le cadre d'une étude de suivi, nous avons ensuite utilisé des différentes expériences d'imageries sur des cellules vivantes et d'immunofluorescences. Celles-ci furent couplées à des micromanipulations de la taille des cellules, des techniques modifiant l'adhésion cellulaire et des approches de knock-down des protéines pour étudier les mécanismes de régulation de la cytokinèse. Les expériences d'imageries sur cellules vivantes et les micromanipulations du volume cytoplasmique ont démontré que la taille des cellules détermine la vitesse de constriction de l'anneau contractile, c'est-à-dire que la vitesse de constriction devient progressivement plus lente à mesure que la taille des cellules diminue. Cependant, ce phénomène n'a lieu que lorsque les embryons atteignent le stade de 16 cellules ce qui suggère qu'une limite supérieure de vitesse de constriction peut exister pour restreindre l’augmentation de cette vitesse quand les cellules sont trop grandes. La taille des cellules étant un déterminant de la progression de la cytokinèse, nos expériences de knock-down des protéines ont, de plus, démontré que la formation de la polarité cellulaire a un impact négatif sur l'assemblage et la constriction de l'anneau contractile dans les cellules externes au stade de morula. Plus précisément, nous avons constaté que la polarité limite le recrutement des composants de la cytokinèse spécifiquement d'un côté de l'anneau contractile, provoquant ainsi un déséquilibre de l’ingression du sillon de clivage et réduisant la vitesse de constriction dans les cellules externes. Nous spéculons que la polarité cellulaire agit comme un obstacle à la progression de la cytokinèse, rendant ainsi les cellules externes plus sensibles à un échec de la cytokinèse. Ces études ont démontré un nouveau mécanisme par lequel la tétraploïdie conduit à l’instabilité chromosomique et à l’aneuploïdie chez les embryons. Ainsi un défaut de la dynamique de correction de l’attachement des kinétochores aux microtubules entraîne une mauvaise ségrégation des chromosomes indépendamment à la formation des fuseaux multipolaires. Ce travail a mis en évidence un rôle inhibiteur de la polarité apicale inattendu sur la machinerie cytokinétique. Cette inhibition pourrait fournir une explication mécanistique de l’incidence élevée de la binucléation dans le trophectoderme. Dans l'ensemble, ces résultats contribuent à notre compréhension du contrôle spatio-temporel de la cytokinèse au cours du développement embryonnaire et fournissent de nouvelles informations mécanistiques sur les origines et les conséquences biologiques de la tétraploïdie chez les embryons préimplantatoires. Les résultats présentés dans cette thèse ont des implications cliniques importantes, puisqu’ils fournissent des preuves définitives que la tétraploïdie générée par un échec de la cytokinèse est délétère pour le développement embryonnaire. Ces travaux mettent ainsi en lumière que la binucléation est un critère de sélection embryonnaire important à considérer lors des traitements de fertilité.Cell division is comprised of mitosis and cytokinesis and is an essential biological process for the maintenance of healthy organisms. During mitosis, a bipolar spindle is assembled, and the chromosomes are aligned at the metaphase plate via the attachment of kinetochores to spindle microtubules. Once chromosome alignment is achieved, the sister chromatids are pulled apart by the microtubules during anaphase and segregated into the nascent daughter cells. Cytokinesis is initiated after anaphase onset and marks the completion of cell division by partitioning the cytoplasm of the dividing cell into two new daughter cells. Successful and timely completion of both mitosis and cytokinesis is key for the maintenance of genome integrity, and failure in either one of these processes affects genetic fidelity. Whereas chromosome segregation errors in mitosis can lead to whole chromosome gains or losses, termed aneuploidy, cytokinesis failure leads to the formation of a binucleated cell with an entirely duplicated genome, termed tetraploidy. In somatic cells, tetraploidy can either lead to cell cycle arrest and death or cause chromosomal instability (CIN), thereby promoting the proliferation of cells with high tumorigenic potential. Therefore, understanding cytokinesis regulation and the potential causes of cytokinesis failure is key, especially in the context of multicellular embryonic systems, wherein progressive cell size reductions coincide with developmental transitions. Moreover, binucleation is frequently observed in human embryos in fertility clinics, and whether binucleation impacts early divisions remains elusive. To elucidate the consequences of tetraploidy, we used the mouse embryo as a model and employed high-resolution immunofluorescence and live-cell imaging experiments. We found that tetraploidy in mouse embryos causes CIN and aneuploidy by a mechanism distinct from that of somatic cells. Whereas in somatic cells multipolar spindle formation caused by supernumerary centrosomes is the major mechanism by which tetraploidy leads to CIN, in mouse embryos - which are acentriolar – tetraploidy does not lead to multipolar spindle formation. Instead, mouse tetraploid embryos develop CIN due to reduced microtubule turnover and impaired error correction activity, which prevents the timely resolution of kinetochore-microtubule mis-attachments, thereby leading to high levels of chromosome segregation errors. As a follow-up study, we next employed live imaging and immunofluorescence experiments, coupled with micromanipulations of cell size, cell adhesion and protein knockdown approaches to investigate the regulatory mechanisms of cytokinesis. Live imaging experiments and micromanipulations of cytoplasmic volume demonstrated that cell size determines the speed of contractile ring constriction i.e., constriction speed becomes progressively slower as the cells decrease in size. However, this phenomenon takes place only when embryos reach the 16-cell stage, suggesting that an upper limit of constriction speed may exist to restrict the scalability of ring constriction to cell size. In addition to cell size being a powerful determinant of cytokinesis progression, our loss-of-function experiments revealed that the emergence of cell polarity negatively impacts contractile ring assembly and constriction in outer cells at the morula stage. More specifically, we found that polarity limits the recruitment of cytokinesis components specifically to one side of the contractile ring, thereby causing unbalanced furrow ingression and reducing constriction speed in outer cells. We speculate that cell polarity may act as an obstacle for cytokinesis progression and render outer cells to be more susceptible to cytokinesis failure. These studies have revealed a novel mechanism by which tetraploidy leads to chromosomal instability and aneuploidy in embryos, wherein defective kinetochore-microtubule dynamics cause chromosome mis-segregation in a manner independent of multipolar spindle formation. In addition, this work unravelled an unexpected inhibitory role of apical polarity on the cytokinetic machinery that might provide a mechanistic explanation for the high incidences of binucleation in the outer layer of blastocysts. Altogether, these findings contribute to our understanding of the spatiotemporal control of cytokinesis during embryonic development and provide new mechanistic insights into the origins and biological consequences of tetraploidy in preimplantation embryos. The results presented in this thesis have substantial clinical implications, as they provide definitive evidence that tetraploidy generated by cytokinesis failure is deleterious to embryonic development, therefore underlining binucleation as an important embryo selection criterion to be considered during fertility treatments

An automated fluorescence lifetime imaging multiwell plate reader: application to high content imaging of protein interactions and label free readouts of cellular metabolism

This thesis reports on work performed in the development and application of an automated plate reading microscope implementing wide field time gated fluorescence lifetime imaging technology. High content analysis (HCA) imaging assays enabled by automated microscopy platforms allow hundreds of conditions to be tested in a single experiment. Though fluorescence lifetime imaging (FLIM) is established in life sciences applications as a method whereby quantitative information may be extracted from time-resolved fluorescence signals, FLIM has not been widely adopted in an HCA context. The FLIM plate reader developed throughout this PhD has been designed to allow HCA-FLIM experiments to be performed and has been demonstrated to be capable of recording multispectral, FLIM and bright field data from 600 fields of view in less than four hours. FLIM is commonly used as a means of reading out Förster resonance energy transfer (FRET) between fluorescent fusion proteins in cells. Using the FLIM plate reader to investigate large populations of cells per experimental condition without significant user input has allowed statistically significant results to be obtained in FRET experiments that present relatively small changes in mean fluorescent lifetime. This capability has been applied to investigations of FOXM1 SUMOylation in response to anthracycline treatment, and to studies of the spatiotemporal activation profiles of small GTPases. Furthermore, the FLIM plate reader allows FLIM-FRET to be applied to protein-protein interaction screening. The application of the instrument to screening RASSF proteins for interaction with MST1 is discussed. The FLIM plate reader was also configured to utilise ultraviolet excitation radiation and optimised for the measurement of autofluorescence lifetime for label-free assays of biological samples. Experiments investigating the autofluorescence lifetime of live cells under the influence of metabolic modulators are presented alongside the design considerations necessary when using UV excitation for HCA-FLIM.Open Acces

Probabilistic Tracking and Behavior Identification of Fluorescent Particles

Explicit and tractable characterizations of the dynamical behavior of virus particles are pivotal for a thorough understanding of the infection mechanisms of viruses. This thesis deals with the problem of extracting symbolic representations of the dynamical behavior of fluorescent particles from fluorescence microscopy image sequences. The focus is on the behavior of virus particles such as fusion with the cell membrane. A numerical representation is obtained by tracking the particles in the image sequences. We have investigated probabilistic tracking approaches, including approaches based on the Kalman filter as well as based on particle filters. For reasons of efficiency and robustness, we developed a tracking approach based on the probabilistic data association (PDA) algorithm in combination with an ellipsoidal sampling scheme that exploits effectively the image data via parametric appearance models. To track objects in close proximity, we compute the support that each image position provides to each tracked object relative to the support provided to the object's neighbors. After tracking, the problem of mapping the trajectory information computed by the tracking approaches to symbolic representations of the behavior arises. To compute symbolic representations of behaviors related to the fusion of single virus particles with the cell membrane based on their intensity over time, we developed a layered probabilistic approach based on stochastic hybrid systems as well as hidden Markov models (HMMs). We use a maxbelief strategy to efficiently combine both representations. The layered approach describes the intensity, intensity models, and behaviors of single virus particles. We introduce models for the evolution of the intensity and the behavior. To compute estimates for the intensity, intensity models, and behaviors we use a hybrid particle filter and the Viterbi algorithm. The developed approaches have been applied to synthetic images as well as to real microscopy image sequences displaying human immunodeficiency virus (HIV-1) particles. We have performed an extensive quantitative evaluation of the performance and a comparison with several existing approaches. It turned out that our approaches outperform previous ones, thus yielding more accurate and more reliable information about the behavior of virus particles. Moreover, we have successfully applied our tracking approaches to 3D image sequences displaying herpes simplex virus (HSV) replication compartments. We also applied the tracking approaches to image data displaying microtubule tips and analyzed their motion. In addition, our tracking approaches were successfully applied to the 2D and 3D image data of a Particle Tracking Challenge

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

Lab-on-CMOS Sensors and Real-time Imaging for Biological Cell Monitoring

Monitoring biological cell growth and viability is essential for in vivo biomedical diagnosis and therapy, and in vitro studies of pharmaceutical efficacy and material toxicity. Conventional monitoring techniques involve the use of dyes and markers that can potentially introduce side effects into the cell culture and often function as end-point assays. This eliminates the opportunity to track fast changes and to determine temporal correlation between measurements. Particularly in drug screening applications, high-temporal resolution cell viability data could inform decisions on drug application protocols that could lead to better treatment outcomes. This work presents development of a lab-on-chip (LoC) sensor for real-time monitoring of biological cell viability and proliferation, to provide a comprehensive picture of the changes cells undergo during their lifecycle. The LoC sensor consists of a complementary metal-oxide-semiconductor (CMOS) chip that measures the cell-to-substrate coupling of adherent cells that are cultured directly on top. This technique is non-invasive, does not require biochemical labeling, and allows for automated and unsupervised cell monitoring. The CMOS capacitance sensor was designed to addresses the ubiquitous challenges of sensitivity, noise coupling, and dynamic range that affect existing sensors. The design includes on-chip digitization, serial data output, and programmable control logic in order to facilitate packaging requirements for biological experiments. Only a microcontroller is required for readout, making it suitable for applications outside the traditional laboratory setting. An imaging platform was developed to provide time-lapse images of the sensor surface, which allowed for concurrent visual and capacitance observation of the cells. Results showed the ability of the LoC sensor to detect single cell binding events and changes in cell morphology. The sensor was used in in vitro experiments to monitor chemotherapeutic agent potency on drug-resistant and drug-sensitive cancer cell lines. Concentrations higher than 5 μM elicited cytotoxic effects on both cell lines, while a dose of 1 μM allowed discrimination of the two cell types. The system demonstrates the use of real-time capacitance measurements as a proof-of-concept tool that has potential to hasten the drug development process

Computational phase imaging for biomedical applications

When a sample is illuminated by an imaging field, its fingerprints are left on the amplitude and the phase of the emerging wave. Capturing the information of the wavefront grants us a deeper understanding of the optical properties of the sample, and of the light-matter interaction. While the amplitude information has been intensively studied, the use of the phase information has been less common. Because all detectors are sensitive to intensity, not phase, wavefront measurements are significantly more challenging. Deploying optical interferometry to measure phase through phase-intensity conversion, quantitative phase imaging (QPI) has recently gained tremendous success in material and life sciences. The first topic of this dissertation describes our effort to develop a new QPI setup, named transmission Spatial Light Interference Microscopy (tSLIM), that uses the twisted nematic liquid-crystal (TNLC) modulators. Compared to the established SLIM technique, tSLIM is much less expensive to build than its predecessor (SLIM) while maintaining significant performance. The tSLIM system uses parallel aligned liquid-crystal (PANLC) modulators, has a slightly smaller signal-to-noise Ratio (SNR), and a more complicated model for the image formation. However, such complexity is well addressed by computing. Most importantly, tSLIM uses TNLC modulators that are popular in display LCDs. Therefore, the total cost of the system is significantly reduced. Alongside developing new imaging modalities, we also improved current QPI imaging systems. In practice, an incident field to the sample is rarely perfectly spatially coherent, i.e., plane wave. It is generally partially coherent; i.e., it comprises of many incoherent plane waves coming from multiple directions. This illumination yields artifacts in the phase measurement results, e.g., halo and phase-underestimation. One solution is using a very bright source, e.g., a laser, which can be spatially filtered very well. However, the laser comes at the expense of speckles, which degrades image quality. Therefore, solutions purely based on physical modeling and computations to remove these artifacts, using white-light illumination, are highly desirable. Here, using physical optics, we develop a theoretical model that accurately explains the effects of partial coherence on image information and phase information. The model is further combined with numerical processing to suppress the artifacts, and recover the correct phase information. The third topic is devoted to applying QPI to clinical applications. Traditionally, stained tissues are used in prostate cancer diagnosis instead. The reason is that tissue samples used in diagnosis are nearly transparent under bright field inspection if unstained. Contrast-enhanced microscopy techniques, e.g., phase contrast microscopy (PC) and differential interference contrast microscopy (DIC), can render visibility of the untagged samples with high throughput. However, since these methods are intensity-based, the contrast of acquired images varies significantly from one imaging facility to another, preventing them from being used in diagnosis. Inheriting the merits of PC, SLIM produces phase maps, which measure the refractive index of label-free samples. However, the maps measured by SLIM are not affected by variation in imaging conditions, e.g., illumination, magnification, etc., allowing consistent imaging results when using SLIM across different clinical institutions. Here, we combine SLIM images with machine learning for automatic diagnosis results for prostate cancer. We focus on two diagnosis problems of automatic Gleason grading and cancer vs. non-cancer diagnosis. Finally, we introduce a new imaging modality, named Gradient Light Interference Microscopy (GLIM), which is able to image through optically thick samples using low spatial coherence illumination. The key benefit of GLIM comes from a large numerical aperture of the condenser, which is 0.55 NA, about five times higher than that in SLIM. GLIM has an excellent depth sectioning when recording three-dimensional information of the susceptibility of the sample. We also introduce a model for the image formation of GLIM with an implication that a simple filtering step in the transverse dimension can dramatically improve the sectioning in the axial dimension. With GLIM, one can measure accurately the surface area, volume, and dry mass of a variety of biological samples, ranging from cells that are about tens of microns thick to bovine embryos that are hundreds of microns thick

Removal of antagonistic spindle forces can rescue metaphase spindle length and reduce chromosome segregation defects

Regular Abstracts - Tuesday Poster Presentations: no. 1925Metaphase describes a phase of mitosis where chromosomes are attached and oriented on the bipolar spindle for subsequent segregation at anaphase. In diverse cell types, the metaphase spindle is maintained at a relatively constant length. Metaphase spindle length is proposed to be regulated by a balance of pushing and pulling forces generated by distinct sets of spindle microtubules and their interactions with motors and microtubule-associated proteins (MAPs). Spindle length appears important for chromosome segregation fidelity, as cells with shorter or longer than normal metaphase spindles, generated through deletion or inhibition of individual mitotic motors or MAPs, showed chromosome segregation defects. To test the force balance model of spindle length control and its effect on chromosome segregation, we applied fast microfluidic temperature-control with live-cell imaging to monitor the effect of switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. We show that spindle midzone proteins kinesin-5 cut7p and microtubule bundler ase1p contribute to outward pushing forces, and spindle kinetochore proteins kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Our results stress the importance of proper chromosome-to-microtubule attachment over spindle length regulation for proper chromosome segregation.postprin

Psr1p interacts with SUN/sad1p and EB1/mal3p to establish the bipolar spindle

Regular Abstracts - Sunday Poster Presentations: no. 382During mitosis, interpolar microtubules from two spindle pole bodies (SPBs) interdigitate to create an antiparallel microtubule array for accommodating numerous regulatory proteins. Among these proteins, the kinesin-5 cut7p/Eg5 is the key player responsible for sliding apart antiparallel microtubules and thus helps in establishing the bipolar spindle. At the onset of mitosis, two SPBs are adjacent to one another with most microtubules running nearly parallel toward the nuclear envelope, creating an unfavorable microtubule configuration for the kinesin-5 kinesins. Therefore, how the cell organizes the antiparallel microtubule array in the first place at mitotic onset remains enigmatic. Here, we show that a novel protein psrp1p localizes to the SPB and plays a key role in organizing the antiparallel microtubule array. The absence of psr1+ leads to a transient monopolar spindle and massive chromosome loss. Further functional characterization demonstrates that psr1p is recruited to the SPB through interaction with the conserved SUN protein sad1p and that psr1p physically interacts with the conserved microtubule plus tip protein mal3p/EB1. These results suggest a model that psr1p serves as a linking protein between sad1p/SUN and mal3p/EB1 to allow microtubule plus ends to be coupled to the SPBs for organization of an antiparallel microtubule array. Thus, we conclude that psr1p is involved in organizing the antiparallel microtubule array in the first place at mitosis onset by interaction with SUN/sad1p and EB1/mal3p, thereby establishing the bipolar spindle.postprin

Towards increased efficiency and automation in fluorescence micrograph analysis based on hand-labeled data

Held CH. Towards increased efficiency and automation in fluorescence micrograph analysis based on hand-labeled data. Bielefeld: Universität Bielefeld; 2013.In the past decade, automation in fluorescence microscopy has strongly increased, particularly in regards to image acquisition and sample preparation, which results in a huge volume of data. The amount of time required for manual assessment of an experiment is hence mainly determined by the amount of time required for data analysis. In addition, manual data analysis is often a task with poor reproducibility and lack of objectivity. Using automated image analysis software, the time required for data analysis can be reduced while quality and reproducibility of the evaluation are improved. Most image analysis approaches are based on a segmentation of the image. By arranging several image processing methods in a so-called segmentation pipeline, and by adjusting all parameters, a broad range of fluorescence image data can be segmented. The drawback of available software tools is the long time required to calibrate the segmentation pipeline for an experiment, particularly for researchers with little knowledge of image processing. As a result, many experiments that could benefit from automated image analysis are still evaluated manually. In order to reduce the amount of time users have to spend in adapting automated image analysis software to their data, research was carried out on a novel image analysis concept based on hand-labeled data. Using this concept, the user is required to provide hand-labeled cells, based on which an efficient combination of image processing methods and their parameterization is automatically calibrated, without further user input. The development of a segmentation pipeline that allows high-quality segmentation of a broad range of fluorescence micrographs in short time poses a challenge. In this work, a three-stage segmentation pipeline consisting of exchangeable preprocessing, figure-ground separation and cell-splitting methods was developed. These methods are mainly based on the state of the art, whereas some of them represent contributions to this status. Discretization of parameters must be performed carefully, as a broad range of fluorescence image data shall be supported. In order to allow calibration of the segmentation pipeline in a short time, discretization with equidistant as well as nonlinear step sizes was implemented. Apart from parameter discretization, quality of the calibration strongly depends on choice of the parameter optimization technique. In order to reduce calibration runtime, exploratory parameter space analysis was performed for different segmentation methods. This experiment showed that parameter spaces are mostly monotonous, but also show several local performance maxima. The comparison of different parameter optimization techniques indicated that the coordinate descent method results in a good parameterization of the segmentation pipeline in a small amount of time. In order to minimize the amount of time spent by the user in calibration of the system, correlation between the number of hand-labeled reference samples and the resulting segmentation performance was investigated. This experiment demonstrates that as few as ten reference samples often result in a good parameterization of the segmentation pipeline. Due to the low number of cells required for automatic calibration of the segmentation pipeline, as well as its short runtime, it can be concluded that the investigated method improves automation and efficiency in fluorescence micrograph analysis