A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images

Nasser, Lamees; Boudier, Thomas

doi:10.1038/s41598-019-41683-3

Cited by 12 publications

(11 citation statements)

References 50 publications

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“…Spheroids volume was the sum of all the volumes (area x 1 μm (resolution of the z-stack)) of spheroids in each stack. The quantification of nuclei in 3D spheroids for DAPI, Ki-67, and caspase 3 analysis was done using our dictionary-based denoising method to segment, detect, and calculate the total cell nuclei in 3D stacked images of a spheroid ( Nasser and Boudier, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

The role of cell-matrix adhesion and cell migration in breast tumor growth and progression

Chong,

Yip,

Farm

et al. 2024

Front. Cell Dev. Biol.

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During breast cancer progression, there is typically increased collagen deposition resulting in elevated extracellular matrix rigidity. This results in changes to cell-matrix adhesion and cell migration, impacting processes such as the epithelial-mesenchymal transition (EMT) and metastasis. We aim to investigate the roles of cell-matrix adhesion and cell migration on breast tumor growth and progression by studying the impacts of different types of extracellular matrices and their rigidities. We embedded MCF7 spheroids within three-dimensional (3D) collagen matrices and agarose matrices. MCF7 cells adhere to collagen but not agarose. Contrasting the results between these two matrices allows us to infer the role of cell-matrix adhesion. We found that MCF7 spheroids exhibited the fastest growth rate when embedded in a collagen matrix with a rigidity of 5.1 kPa (0.5 mg/mL collagen), whereas, for the agarose matrix, the rigidity for the fastest growth rate is 15 kPa (1.0% agarose) instead. This discrepancy is attributable to the presence of cell adhesion molecules in the collagen matrix, which initiates collagen matrix remodeling and facilitates cell migration from the tumor through the EMT. As breast tumors do not adhere to agarose matrices, it is suitable to simulate the cell-cell interactions during the early stage of breast tumor growth. We conducted further analysis to characterize the stresses exerted by the expanding spheroid on the agarose matrix. We identified two distinct MCF7 cell populations, namely, those that are non-dividing and those that are dividing, which exerted low and high expansion stresses on the agarose matrix, respectively. We confirmed this using Western blot which showed the upregulation of proliferating cell nuclear antigen, a proliferation marker, in spheroids grown in the 1.0% agarose (≈13 kPa). By treating the embedded MCF7 spheroids with an inhibitor or activator of myosin contractility, we showed that the optimum spheroids’ growth can be increased or decreased, respectively. This finding suggests that tumor growth in the early stage, where cell-cell interaction is more prominent, is determined by actomyosin tension, which alters cell rounding pressure during cell division. However, when breast tumors begin generating collagen into the surrounding matrix, collagen remodeling triggers EMT to promote cell migration and invasion, ultimately leading to metastasis.

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Section: Methodsmentioning

confidence: 99%

The role of cell-matrix adhesion and cell migration in breast tumor growth and progression

Chong,

Yip,

Farm

et al. 2024

Front. Cell Dev. Biol.

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“…Segmenting cell nuclei within spheroids is usually the first step for single-cell quantitative analysis. Many classic pipelines rely on initial thresholding, followed by watershed algorithms to separate adjacent nuclei [ 111 , 149 ]. Alternatively, this can be achieved by machine and deep learning methods.…”

Section: Imaging and Analysis Of Mctsmentioning

confidence: 99%

Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis

Mitrakas

Tsolou

Didaskalou

et al. 2023

IJMS

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Biomedical research requires both in vitro and in vivo studies in order to explore disease processes or drug interactions. Foundational investigations have been performed at the cellular level using two-dimensional cultures as the gold-standard method since the early 20th century. However, three-dimensional (3D) cultures have emerged as a new tool for tissue modeling over the last few years, bridging the gap between in vitro and animal model studies. Cancer has been a worldwide challenge for the biomedical community due to its high morbidity and mortality rates. Various methods have been developed to produce multicellular tumor spheroids (MCTSs), including scaffold-free and scaffold-based structures, which usually depend on the demands of the cells used and the related biological question. MCTSs are increasingly utilized in studies involving cancer cell metabolism and cell cycle defects. These studies produce massive amounts of data, which demand elaborate and complex tools for thorough analysis. In this review, we discuss the advantages and disadvantages of several up-to-date methods used to construct MCTSs. In addition, we also present advanced methods for analyzing MCTS features. As MCTSs more closely mimic the in vivo tumor environment, compared to 2D monolayers, they can evolve to be an appealing model for in vitro tumor biology studies.

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“…Another advantage is the simultaneous, efficient, and independent 2P excitation of multiple spectrally distinct chromophores, which enables multi-color imaging using a single mode-locked laser source. Therefore, 2P imaging approaches are being increasingly used in biology for a variety of purposes, such as visualizing specific molecules and recording their activities or signaling events at the subcellular level in multi-color imaging [3][4][5]. Its inherent 3D resolution has also been exploited in a number of studies, wherein it is widely used for high-resolution imaging at the micron and submicron scales in thick biological specimens [6,7].…”

Section: Introductionmentioning

confidence: 99%

Multi‐color two‐photon scanning structured illumination microscopy imaging of live cells

Wang

Chen

et al. 2023

Journal of Biophotonics

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Multi‐color two‐photon microscopy imaging of live cells is essential in biology. However, the limited diffraction resolution of conventional two‐photon microscopy restricts its application to subcellular organelle imaging. Recently, we developed a laser scanning two‐photon non‐linear structured illumination microscope (2P‐NLSIM), whose resolution improved three‐fold. However, its ability to image polychromatic live cells under low excitation power has not been verified. Here, to improve the reconstruction super‐resolution image quality under low excitation power, we increased the image modulation depth by multiplying the raw images with the reference fringe patterns in the reconstruction process. Simultaneously, we optimized the 2P‐NLSIM system to image live cells, including the excitation power, imaging speed, and field of view. The proposed system could provide a new imaging tool for live cells.

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A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images

Cited by 12 publications

References 50 publications

The role of cell-matrix adhesion and cell migration in breast tumor growth and progression

The role of cell-matrix adhesion and cell migration in breast tumor growth and progression

Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis

Multi‐color two‐photon scanning structured illumination microscopy imaging of live cells

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