Biology subjects

Frismantiene, A.

Publications and source records attributed to Frismantiene, A..

3 recordsLinked to original sources

bioRxiv2025

Real-time feedback control microscopy for automation of optogenetic targeting

Optogenetics has revolutionized our ability to study cellular signaling by enabling the precise control of cellular functions with light. Most classical implementations rely on fixed or manually updated illumination patterns, limiting their ability to accommodate living systems that move, change shape or rapidly adapt their signaling states. Here, we present an experimental platform for Feedback Adaptive Real-time Optogenetics (FARO) that combines automated image segmentation, tracking, feature extraction, and adaptive hardware control to dynamically adjust optogenetic stimulation based on live cell behavior. By continuously analyzing biosensor signals, FARO updates illumination patterns in real time across biological scales; from maintaining stimulation on specific subcellular regions, to selectively activating single cells in deforming tissue. This fully automated, Python-based framework is built on open standards for data management and microscope control and data handling, supporting large-scale experiments and long-term timelapse studies, compatible with different microscope hardware. Eliminating the need for human intervention to reposition light patterns or select target cells enables reproducible, systematic and high-throughput interrogation of spatiotemporal signaling. We show how automated and adaptive optogenetic perturbations are a powerful tool to study how local signaling events shape cellular behavior, from subcellular dynamics and single-cell migration up to emergent tissue-level processes.

cell biology↗

bioRxiv2024

Convpaint - Universal framework for interactive pixel classification using pretrained neural networks

We develop Convpaint, a universal computational framework for interactive pixel classification. Convpaint utilizes pretrained convolutional neural networks (CNNs) or vision transformers (ViTs) for feature extraction and enables easy segmentation across a wide variety of tasks. Available within the Python-based napari software ecosystem, Convpaint integrates seamlessly with other plugins into image processing pipelines, which we demonstrate with three workflows across different data modalities.

bioinformatics↗

bioRxiv2021

Optogenetic actuator/biosensor circuits for large-scale interrogation of ERK dynamics identify sources of MAPK signaling robustness.

Combining single-cell measurements of ERK activity dynamics with perturbations provides insights into the MAPK network topology. We built circuits consisting of an optogenetic actuator to activate MAPK signaling and an ERK biosensor to measure single-cell ERK dynamics. This allowed us to conduct RNAi screens to investigate the role of 50 MAPK proteins in ERK dynamics. We found that the MAPK network is robust against most node perturbations. We observed that the ERK-RAF and the ERK-RSK2-SOS negative feedbacks operate simultaneously to regulate ERK dynamics. Bypassing the RSK2-mediated feedback, either by direct optogenetic activation of RAS, or by RSK2 perturbation, sensitized ERK dynamics to further perturbations. Similarly, targeting this feedback in a human ErbB2-dependent oncogenic signaling model increased the efficiency of a MEK inhibitor. The RSK2-mediated feedback is thus important for the ability of the MAPK network to produce consistent ERK outputs and its perturbation can enhance the efficiency of MAPK inhibitors.

systems biology↗