Related papers: Robust 3D Cell Segmentation: Extending the View of…

Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep…

Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…

Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…

In this work, we describe a method for large-scale 3D cell-tracking through a segmentation selection approach. The proposed method is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve problems…

Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation,…

The quantitative analysis of 3D confocal microscopy images of the shoot apical meristem helps understanding the growth process of some plants. Cell segmentation in these images is crucial for computational plant analysis and many automated…

Recent trends in cell segmentation have shifted towards universal models to handle diverse cell morphologies and imaging modalities. However, for continuously emerging cell types and imaging techniques, these models still require hundreds…

Cell segmentation is a fundamental task in microscopy image analysis. Several foundation models for cell segmentation have been introduced, virtually all of them are extensions of Segment Anything Model (SAM), improving it for microscopy…

We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries,…

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…

Medical image segmentation requires not only accuracy but also robustness under challenging imaging conditions. In this study, we show that a carefully configured DeepLabv3 model can achieve high performance in segmenting induced…

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make…

Cells are the fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress…

Deep neural networks have become the go-to method for biomedical instance segmentation. Generalist models like Cellpose demonstrate state-of-the-art performance across diverse cellular data, though their effectiveness often degrades on…

Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly…

We introduce CellSegmenter, a structured deep generative model and an amortized inference framework for unsupervised representation learning and instance segmentation tasks. The proposed inference algorithm is convolutional and…

We present a weakly supervised deep learning method to perform instance segmentation of cells present in microscopy images. Annotation of biomedical images in the lab can be scarce, incomplete, and inaccurate. This is of concern when…

In recent years, several unsupervised cell segmentation methods have been presented, trying to omit the requirement of laborious pixel-level annotations for the training of a cell segmentation model. Most if not all of these methods handle…

To address prevalent issues in medical imaging, such as data acquisition challenges and label availability, transfer learning from natural to medical image domains serves as a viable strategy to produce reliable segmentation results.…

We share our recent findings in an attempt to train a universal segmentation network for various cell types and imaging modalities. Our method was built on the generalized U-Net architecture, which allows the evaluation of each component…