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Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
Bacterial biofilm segmentation poses significant challenges due to lack of apparent structure, poor imaging resolution, limited contrast between conterminous cells and high density of cells that overlap. Although there exist bacterial…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
Lineage tracing, the tracking of living cells as they move and divide, is a central problem in biological image analysis. Solutions, called lineage forests, are key to understanding how the structure of multicellular organisms emerges. We…
Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates…
Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new,…
The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching…
A human watching a video of closely-packed cells can generally identify every individual cell, regardless of density and noise, but most currently-available cell-tracking software cannot. This is because the human brain automatically builds…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
Lineage tracing, the joint segmentation and tracking of living cells as they move and divide in a sequence of light microscopy images, is a challenging task. Jug et al. have proposed a mathematical abstraction of this task, the moral…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
The accurate tracking of live cells using video microscopy recordings remains a challenging task for popular state-of-the-art image processing based object tracking methods. In recent years, several existing and new applications have…
Electron tomography (ET) allows high-resolution reconstructions of macromolecular complexes at nearnative state. Cellular structures segmentation in the reconstruction data from electron tomographic images is often required for analyzing…
Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
We propose a cell segmentation method for analyzing images of densely clustered cells. The method combines the strengths of marker-controlled watershed transformation and a convolutional neural network (CNN). We demonstrate the method…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
Earth's forests play an important role in the fight against climate change, and are in turn negatively affected by it. Effective monitoring of different tree species is essential to understanding and improving the health and biodiversity of…
We propose a novel dynamic image reconstruction method from PET listmode data that could be particularly suited to tracking single or small numbers of cells. In contrast to conventional PET reconstruction our method combines the information…