Automated segmentation of soft X-ray tomography: native cellular structure with sub-micron resolution at high throughput for whole-cell quantitative imaging in yeast

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Abstract Soft X-ray tomography (SXT) is an invaluable tool for quantitatively analyzing cellular structures at sub-optical isotropic resolution. However, it has traditionally depended on manual segmentation, limiting its scalability large datasets. Here, we leverage a deep learning-based auto-segmentation pipeline to segment and label in hundreds of cells across three Saccharomyces cerevisiae strains. This task-based employs iterative refinement improve segmentation accuracy key structures, including the cell body, nucleus, vacuole, lipid droplets, enabling high-throughput precise phenotypic analysis. Using this approach, compared 3D whole-cell morphometric characteristics wild-type, VPH1-GFP, vac14 strains, uncovering detailed strain-specific organelle size shape variations. We show utility SXT data curvature analysis entire organelles detection fine morphological features using surface meshes. Our approach facilitates comparative analyses with high spatial precision statistical throughput, subtle single population level. workflow significantly enhances our ability characterize anatomy supports scalable studies mesoscale, applications investigating architecture, biology, genetic research diverse biological contexts. Significance Statement offers many powerful multi-organelle imaging, but, like other resolution volumetric imaging modalities, typically limited by low throughput due laborious segmentation. Auto-segmentation soft overcomes limitation, multiple whole populations. The combination statistically useful represents avenue more thorough characterizations toto opens new mesoscale questions modeling morphology, interactions, responses perturbations.

Language: Английский

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Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 17, 2024

Abstract A current challenge in bioimaging for immunology and immunotherapy research lies analyzing multimodal multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed high-performance, end-to-end analysis of image-based vitro immune assays. Purpose-built multicondition, 2D multichannel time-lapse microscopy mixed populations, Celldetective is optimized the needs The seamlessly integrates AI-based segmentation, Bayesian tracking, automated single-cell event detection, all within intuitive graphical interface supports interactive visualization, annotation, training capabilities. We demonstrate its utility with original on effector activating surface, mediated by bispecific antibodies, further showcase potential extensive sets pairwise antibody-dependent cytotoxicity events.

Language: Английский

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Cell State-Specific Cytoplasmic Material Properties Control Spindle Architecture and Scaling

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

ABSTRACT Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How physicochemical properties of affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination adaptive feedback microscopy, we investigated mitotic cell morphology during neural differentiation embryonic stem cells. While tubulin microtubule dynamics remained unchanged, changed their scaling behaviour: differentiating cells, were significantly smaller than those equally-sized undifferentiated Integrating phase imaging, biophysical perturbations theory, found that as cells differentiated, became more dilute. The concomitant decrease free activated CPAP (centrosomal P4.1-associated protein) to enhance centrosomal nucleation capacity. As a consequence, mass shifted towards poles at expense bulk, explaining differentiation-associated switch architecture. This study shows state-specific cytoplasmic density tunes Thus, reveal physical major determinant organelle control.

Language: Английский

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Interpretable representation learning for 3D multi-piece intracellular structures using point clouds

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 26, 2024

Abstract A key challenge in understanding subcellular organization is quantifying interpretable measurements of intracellular structures with complex multi-piece morphologies an objective, robust and generalizable manner. Here we introduce a morphology-appropriate representation learning framework that uses 3D rotation invariant autoencoders point clouds. This used to learn representations are independent orientation, compact, easy interpret. We apply our punctate (e.g. DNA replication foci) polymorphic nucleoli). systematically compare image-based across several structure datasets, including synthetic dataset pre-defined rules organization. explore the trade-offs performance different models by performing multi-metric benchmarking efficiency, generative capability, expressivity metrics. find framework, which embraces underlying morphology structures, facilitates unsupervised discovery sub-clusters for each structure. show how approach can also be applied phenotypic profiling using nucleolar images following drug perturbations. implement provide all CytoDL, python package flexible configurable deep experiments.

Language: Английский

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Computing hematopoietic stem and progenitor cell plasticity in response to genetic mutations and environmental stimulations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 7, 2024

Abstract Cell plasticity (CP), describing a dynamic cell state, plays crucial role in maintaining homeostasis during organ morphogenesis, regeneration and damage-to-repair biological process. Single-cell-omics datasets provide unprecedented resource to empowers analysis on CP. Hematopoiesis offers fertile opportunities develop quantitative methods for understanding CP with rich supports from experimental ground-truths. In this study we generated high-quality lineage-negative (Lin − ) single-cell RNA-sequencing under various conditions introduced working pipeline named Snapdragon interrogate naïve disturbed of hematopoietic stem progenitor cells (HSPCs) mutational or environmental challenges. Utilizing embedding UMAP FA, continuum development is visually observed wildtype where the confirms very low Proportion hybrid-cells ( P hc , bias range: 0.4-0.6) transition trajectory. Upon Tet2 mutation, driver leukemia, treatment DSS, an inducer colitis, increased HSPCs was enhanced. Quantitative indicates that mutation enhances HSC self-renewal capability while DSS results enhanced myeloid-skewing trajectory, suggesting their similar but different consequences. We prioritized several transcription factors (i.e EGR family) signaling pathways (i.e. receptors IL1R1 ADRB, inflammation sympathy-sensing respectively) which are responsible alterations. CellOracle-based simulation suggests knocking-out regulons ADRB partially reverses promoted by inflammation. conclusion, provides transcriptomic matrices diversified simulations computational quantifying (247 words) Highlights To guide analysis, introduce quantizable parameter Snapdragon, discriminate naive hematopoiesis; The +/- Lin demonstrates many novel insights, including PHC; trends inflammatory cells; Regulon transcriptional factor EGR1 significantly activated elevated change trajectory; Stress-response-related mediated were obviously challenged

Language: Английский

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A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 19, 2024

The epithelial to mesenchymal transition (EMT) is a widely studied but poorly defined state change due the variety of ways in which it has been characterized cells. There need for reproducible cell model systems that enable integration and comparison different types measured observations cells across many distinct cellular contexts. We present human induced pluripotent stem (hiPS) as such system by demonstrating its utility through comparative analysis hiPS cell-EMT 2D 3D culture geometries. developed live-imaging-based assays directly compare examples changes function (via migration timing), molecular components expression marker proteins), organization reorganization junctions), environment dynamics basement membrane) same experimental system. EMT-related we occurred earlier colonies than lumenoids, likely differences membrane environments associated with vs. initial have made 449 60-hour-long time-lapse movies tools used visualization open-source easily accessible resource future work this field.

Language: Английский

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Introducing FISCAS, a Tool for the Effective Generation of Single Cell MALDI-MSI Data

Journal of the American Society for Mass Spectrometry, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 9, 2024

We introduce Fluorescence Integrated Single-Cell Analysis Script (FISCAS), which combines fluorescence microscopy with MALDI-MSI to streamline single-cell analysis. FISCAS enables automated selection of tight measurement regions, thereby reducing the acquisition off-target pixels, and makes use established algorithms for cell segmentation coregistration rapidly compile spectra. MALDI-compatible staining membranes, nuclei, lipid droplets allows collection data prior on a timsTOF fleX MALDI-2. Usefulness software is demonstrated by example THP-1 cells during stimulated differentiation into macrophages at different time points. In this proof-of-principle study, was used automatically generate mass spectra along wide range morphometric parameters total number roughly 1300 collected 24, 48, 72 h after onset stimulation. Data analysis combined spectrometry shows significant molecular heterogeneity within population each point, indicating an independent individual rather than synchronized mechanism. Here, grouping based their phenotype revealed overall clearer distinction phases delivered increased signals as possible markers compared traditional bulk Utilizing linkage between spectrometric confirmed expected positive correlation droplet signal triacylglyceride (TG), demonstrating usefulness multimodal approach.

Language: Английский

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Cell shape noise strength regulates shape dynamics during EMT-associated cell spreading

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 15, 2024

ABSTRACT Cellular shape is intimately linked to cell function and state, transitions between states are tightly coupled changes. Yet, has been largely overlooked in state studies. Here, we combine morphometric analysis with theoretical modeling molecular perturbations interrogate dynamics during epithelial-to-mesenchymal transition (EMT). Using stochastic inference, extract the morphogenetic landscape underlying EMT. We show that within this landscape, EMT-associated spreading reflects a attractors. Strikingly, observe peak noise strength concomitant spreading, higher accelerates Our framework will be widely applicable quantitative investigations physiology disease. Together, our results identify key role for cellular stochasticity as regulator of change rates, highlight yield rich phenotypic information enhance understanding states.

Language: Английский

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Where physics and biology meet

Current Biology, Journal Year: 2024, Volume and Issue: 34(20), P. R950 - R960

Published: Oct. 1, 2024

Language: Английский

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Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images

npj Systems Biology and Applications, Journal Year: 2024, Volume and Issue: 10(1)

Published: Nov. 6, 2024

Understanding the dynamic states and transitions of heterogeneous cell populations is crucial for addressing fundamental biological questions. High-content imaging provides rich datasets, but it remains increasingly difficult to integrate annotate high-dimensional time-resolved datasets profile population dynamics in different microenvironments. Using hepatic stellate cells (HSCs) LX-2 as model, we proposed a novel analytical strategy image-based integration annotation 2D/3D High-dimensional features were extracted from extensive image cellular identified based on feature profiles. Time-series clustering revealed distinct temporal patterns shape actin cytoskeleton reorganization. We found showed more complex membrane contractile systems with an M-shaped compactness trend 3D culture, while they displayed rapid spreading early 2D culture. This enhances our understanding HSCs heterogeneity extracellular

Language: Английский

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