Chadha, Y. | Search bioRxiv

bioRxiv2024

SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification

The analysis of spot-like structures is a widespread task in microscopy-based cell biology. Existing solutions are typically specific to single applications and do not use multi-dimensional information from 5D datasets. Therefore, experimental scientists often resort to subjective manual annotation. Here, we present SpotMAX, a generalist AI-driven framework for automated spot detection and quantification. SpotMAX leverages the full scope of multi-dimensional datasets with an easy-to-use interface and an embedded framework for cell segmentation and tracking. SpotMAX outperforms state-of-the-art tools, and in some cases, even expert human annotators. We applied SpotMAX across diverse experimental questions, ranging from meiotic crossover events in C. elegans to mitochondrial DNA dynamics in S. cerevisiae and telomere length in mouse stem cells, leading to new biological insights. With its flexibility in integrating AI workflows, we anticipate that SpotMAX will become the standard for spot analysis in microscopy data. Source code: https://github.com/SchmollerLab/SpotMAX

cell biology↗

bioRxiv2024

Single-cell imaging reveals a key role of Bck2 in budding yeast cell size adaptation to nutrient challenges

Cell size is tightly controlled to optimize cell function and varies broadly depending on the organism, cell type, and environment. The budding yeast S. cerevisiae has been successfully used as a model to gain insights into eukaryotic cell size control. Multiple regulators of cell size in steady-state conditions have been identified, such as the G1/S transition activators Cln3 and Bck2 and the inhibitor Whi5. Individual deletions of these regulators result in populations with altered mean cell volumes. However, size homeostasis remains largely intact. Here, we show that although the roles of Bck2 and Cln3 for cell size regulation appear largely redundant in steady-state, a switch from fermentable to non-fermentable growth media reveals a unique role for Bck2 in cell size adaptation to changing nutrients. We use live-cell microscopy and machine learning-assisted image analysis to track single cells and their progeny through the nutrient switch. We find that after the switch, bck2{Delta} cells experience longer cell cycle arrests and more arrest-associated enlargement than wild-type, whi5{Delta} or cln3{Delta} cells, indicating that Bck2 becomes the critical G1/S activator in changing nutrients. Our work demonstrates that studying size regulation during nutrient shifts to mimic the dynamic environments of free-growing microorganisms can resolve apparent redundancies observed in steady-state size regulation.

cell biology↗