The Gain-Control property of Synaptic Dynamics (SD) describes how the response of a neuron, mediated by short-term depression, can be sensitive to proportional changes of stochastic inputs.This has been related to the temporal filtering property of synaptic efficacy.However, the limits of the strength of Gain-Control in relationship to the efficacy have not been explored.This paper meets this gap by simulating networks using two synapses with fast-and slow-decays of efficacy.The results show that the Gain-Control effect decreases with the decay of efficacy.Formally describing this relationship can facilitate the integration of SD into Spiking Neural Networks.

Integrating the modulatory properties of Synaptic Dynamics (SD) into Spiking Neural Networks (SNNs) can enhance their computational capabilities.For improving this integration process, this paper presents a pipeline based on Differential Evolution to tune parameters of SD models.Using reference signals from in vitro experiments, parameters of two models are tuned as study cases: the Tsodyks-Markram and the Modified Stochastic Synaptic Model.The pipeline has an average success rate of 75% and 80% respectively.The outcome is a distribution of parameters for each model, which can be considered as prior knowledge to facilitate the integration of SD models into SNNs.

Reinforcement Learning (RL) agents can solve diverse tasks but often exhibit unsafe behavior. Constrained Markov Decision Processes (CMDPs) address this by enforcing safety constraints, yet existing methods either sacrifice reward maximization or allow unsafe training. We introduce Constrained Trust Region Policy Optimization (C-TRPO), which reshapes the policy space geometry to ensure trust regions contain only safe policies, guaranteeing constraint satisfaction throughout training. We analyze its theoretical properties and connections to TRPO, Natural Policy Gradient (NPG), and Constrained Policy Optimization (CPO). Experiments show that C-TRPO reduces constraint violations while maintaining competitive returns.

In biology, we are often confronted with information-rich, large-scale trajectory data, but exploring and communicating patterns in such data can be a cumbersome task. Ideally, the data should be wrapped with an interactive visualisation in one concise packet that makes it straightforward to create and test hypotheses collaboratively. To address these challenges, we have developed a tool, linus, which makes the process of exploring and sharing 3D trajectories as easy as browsing a website. We provide a python script that reads trajectory data, enriches them with additional features such as edge bundling or custom axes, and generates an interactive web-based visualisation that can be shared online. linus facilitates the collaborative discovery of patterns in complex trajectory data.

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations.

MOTIVATION: Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time. RESULTS: We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes. AVAILABILITY AND IMPLEMENTATION: The Matlab source code is available at http://treschgroup.de/Genealogies.html.

MOTIVATION: Mouse embryonic stem cells (mESCs) have developed into a prime system to study the regulation of pluripotency in stable cell lines. It is well recognized that different, established protocols for the maintenance of mESC pluripotency support morphologically and functionally different cell cultures. However, it is unclear how characteristic properties of cell colonies develop over time and how they are re-established after cell passage depending on the culture conditions. Furthermore, it appears that cell colonies have an internal structure with respect to cell size, marker expression or biomechanical properties, which is not sufficiently understood. The analysis of these phenotypic properties is essential for a comprehensive understanding of mESC development and ultimately requires a bioinformatics approach to guarantee reproducibility and high-throughput data analysis. RESULTS: We developed an automated image analysis and colony tracking framework to obtain an objective and reproducible quantification of structural properties of cell colonies as they evolve in space and time. In particular, we established a method that quantifies changes in colony shape and (internal) motion using fluid image registration and image segmentation. The methodology also allows to robustly track motion, splitting and merging of colonies over a sequence of images. Our results provide a first quantitative assessment of temporal mESC colony formation and estimates of structural differences between colony growth under different culture conditions. Furthermore, we provide a stream-based visualization of structural features of individual colonies over time for the whole experiment, facilitating visual comprehension of differences between experimental conditions. Thus, the presented method establishes the basis for the model-based analysis of mESC colony development. It can be easily extended to integrate further functional information using fluorescence signals and differentiation markers. AVAILABILITY: The analysis tool is implemented C++ and Mathematica 8.0 (Wolfram Research Inc., Champaign, IL, USA). The tool is freely available from the authors. We will also provide the source code upon request. CONTACT: [email protected].

We have focused our interest on the registration of brightfield transmitted light microscopy images with respect to different histological stainings. For this kind of registration problem we have developed a new segmentation procedure. Based on the obtained consistent segmentations, a nonlinear registration transformation is computed. The applied registration procedure uses a curvature-based nonlinear partial differential equation in order to find the appropriate mapping between the images. We present an example for the registration of images of two consecutive histological sections from a uterine cervix specimen, where one section stained with p16INK4awas mapped onto another with H&E staining. Finally, we give an illustrative example for a tissue volume reconstruction based on an alternately stained large serial section.