Dagmar Iber

Last Name

Iber

First Name

Dagmar

ORCID

0000-0001-8051-1035

Organisational unit

03791 - Iber, Dagmar / Iber, Dagmar

Show all metadata

Search Results

Publications1 - 10 of 58

FollicleFinder: automated three-dimensional segmentation of human ovarian follicles
Yamauchi, Kevin; Biniasch, Marieke; Franz, Leopold; et al. (2022)
bioRxiv
In vitro fertilization (IVF) treatment protocols require frequent monitoring of the ovarian follicle growth process. We report FollicleFinder, an open source pipeline for the automated, 3D segmentation of ovarian follicles. FollicleFinder also accurately measures clinically-relevant morphological properties such as diameter, surface area, and volume.
Relationship between epithelial organization and morphogen interpretation
Iber, Dagmar; Vetter, Roman (2022)
Current Opinion in Genetics & Development
Despite molecular noise and genetic differences between individuals, developmental outcomes are remarkably constant. Decades of research has focused on the underlying mechanisms that ensure this precision and robustness. Recent quantifications of chemical gradients and epithelial cell shapes provide novel insights into the basis of precise development. In this review, we argue that these two aspects may be linked in epithelial morphogenesis.
Morphogen gradients can convey position and time in growing tissues
Vetter, Roman; Iber, Dagmar (2025)
Newton
During embryonic development, cells coordinate fate decisions based on both position and time. While morphogen gradients have long been recognized as a source of positional information, how timing is synchronized across developing tissues remains unclear. We propose a simple mechanism by which morphogen dynamics can also encode time. If the morphogen source expands with a uniformly growing tissue and the gradient maintains a constant decay length, cells experience transient, hump-shaped signals that convey timing cues. Moreover, when two opposing exponential gradients with equal lengths—such as those in the vertebrate neural tube—interact, their product forms a uniform signal that can synchronize fate decisions across the entire tissue. With increasing gradient amplitudes, cells encounter a transient signal; with constant amplitudes, the signal decays—a feature of a depletion timer. This mechanism provides a generalizable principle by which morphogen gradients may coordinate both spatial and temporal aspects of patterning during development.
PINNverse: Accurate parameter estimation in differential equations from noisy data with constrained physics-informed neural networks
Almanstötter, Marius; Vetter, Roman; Iber, Dagmar (2025)
arXiv
Parameter estimation for differential equations from measured data is an inverse problem prevalent across quantitative sciences. Physics-Informed Neural Networks (PINNs) have emerged as effective tools for solving such problems, especially with sparse measurements and incomplete system information. However, PINNs face convergence issues, stability problems, overfitting, and complex loss function design. Here we introduce PINNverse, a training paradigm that addresses these limitations by reformulating the learning process as a constrained differential optimization problem. This approach achieves a dynamic balance between data loss and differential equation residual loss during training while preventing overfitting. PINNverse combines the advantages of PINNs with the Modified Differential Method of Multipliers to enable convergence on any point on the Pareto front. We demonstrate robust and accurate parameter estimation from noisy data in four classical ODE and PDE models from physics and biology. Our method enables accurate parameter inference also when the forward problem is expensive to solve.
The control of lung branching morphogenesis
Iber, Dagmar (2021)
Current Topics in Developmental Biology ~ Cellular Networks in Development
Branching morphogenesis generates epithelial trees which facilitate gas exchange, filtering, as well as secretion processes with their large surface to volume ratio. In this review, we focus on the developmental mechanisms that control the early stages of lung branching morphogenesis. Lung branching morphogenesis involves the stereotypic, recurrent definition of new branch points, subsequent epithelial budding, and lung tube elongation. We discuss current models and experimental evidence for each of these steps. Finally, we discuss the role of the mesenchyme in determining the organ-specific shape.
FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells
Sharma, Abhishek; Meer, Marco; Dapkunas, Arvydas; et al. (2022)
Development
Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a novel function of FGF8. By combining transgenic mouse models, quantitative imaging assays, and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPC behaviour to condensate at the UB. Chemokinetic effects have also been described for other FGFs and may be generally important for the formation of mesenchymal condensates.
Time-lapse and cleared imaging of mouse embryonic lung explants to study three-dimensional cell morphology and topology dynamics
Gómez, Harold Fernando; Doumpas, Nikolaos; Iber, Dagmar (2023)
STAR Protocols
Here, we present a protocol for collecting high-spatiotemporal-resolution datasets of undisturbed mouse embryonic epithelial rudiments using light-sheet fluorescence microscopy. We describe steps for rudiment dissection, clearing, and embedding for cleared and live imaging. We then detail procedures for light-sheet imaging followed by image processing and morphometric analysis. We provide protocol variations for imaging both growing and optically cleared lung explants to encourage the quantitative exploration of three-dimensional cell shapes, cell organization, and complex cell-cell dynamics. For complete details on the use and execution of this protocol, please refer to Gómez et al. (2021).1
PolyHoop: Soft particle and tissue dynamics with topological transitions
Vetter, Roman; Runser, Steve; Iber, Dagmar (2023)
arXiv
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable of simulating a wide range of particulate soft matter systems: from biological cells and tissues to vesicles, bubbles, foams, emulsions, and other amorphous materials. The soft particles or cells are represented by continuously remodeling, non-convex, high-resolution polygons that can undergo growth, division, fusion, aggregation, and separation. With PolyHoop, a tissue or foam consisting of a million cells with high spatial resolution can be simulated on conventional laptop computers.
The impact of cell size on morphogen gradient precision
Adelmann, Jan A.; Vetter, Roman; Iber, Dagmar (2023)
Development
Tissue patterning during embryonic development is remarkably precise. Here, we numerically determine the impact of the cell diameter, gradient length and the morphogen source on the variability of morphogen gradients. We show that the positional error increases with the gradient length relative to the size of the morphogen source, and with the square root of the cell diameter and the readout position. We provide theoretical explanations for these relationships, and show that they enable high patterning precision over developmental time for readouts that scale with expanding tissue domains, as observed in the Drosophila wing disc. Our analysis suggests that epithelial tissues generally achieve higher patterning precision with small cross-sectional cell areas. An extensive survey of measured apical cell areas shows that they are indeed small in developing tissues that are patterned by morphogen gradients. Enhanced precision may thus have led to the emergence of pseudostratification in epithelia, a phenomenon for which the evolutionary benefit had so far remained elusive.
Reduction of a detailed biological signaling model
Iber, Dagmar (2010)
Procedia Computer Science
Biological signaling is complex. Even if only few components are involved models for biological signaling, in general, comprise a large number of variables and parameters to achieve predictive power. This is due to the many states that can be attained even with few components due to the formation of (allosteric) complexes. This phenomenon is generally referred to as combinatorical complexity. Although the detailed parameterized and validated models can be analysed to reveal regulatory principles these models are, in general, too complex to achieve an intuitive understanding. Methods are urgently needed to achieve meaningful model reduction. Ideally, biologists would like models that retain the simplicity of the typical signaling cartoon, yet provide novel insight. We suggest a 2-step process to achieve this. In a first step a large detailed model is developed and tested based on experimental data. In a second step the detailed information gained from the validated model is used to develop a realistic phenomenological model. The procedure is illustrated by example of σF activation during sporulation in Bacillus subtilis. The reduced model indeed successfully reproduces key regulatory aspects of the detailed model and shows how the the exceptional sensitivity of the regulatory network results from the particular allosteric interactions between SpoIIAB (AB), SpoIIAA (AA), and σF and from the sequestration of AB in inactive AB-ADP-AA complexes.

Publications1 - 10 of 58

Dagmar Iber

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results