Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces

By Alexandre Cecilien Dufour, V. Shinin, S. Tajbakhsh, Nancy Guillén-Aghion, Jean-Christophe Olivo-Marin, Christophe Zimmer. 2005

340 citations recorded by the source corpus.

Subfields: Biophysics, Computer Vision and Pattern Recognition

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Citations in the corpus

A benchmark for comparison of cell tracking algorithms (2014, methodology): “After the ISBI 2013 workshop, the organizing committee confirmed the accuracy of the submitted results and compiled the final rankings presented in this article.”
Tracking in cell and developmental biology. (2009, background): “If these conditions are not met, or they need to be compromised for practical reasons, more sophistication is required, such as the use of gradient-vector flows [36, 52], estimated cell dynamics [39, 42], and special procedures to handle cell contacts, divisions, appearances, and disappearances [41,”
Cell Population Tracking and Lineage Construction with Spatiotemporal Context (2007, methodology): “Geometric active contour models implemented via the level set method (Osher and Sethian, 1988) have recently been investigated for cell tracking applications (Mukherjee et al., 2004; Yang et al., 2005a; Dufour et al., 2005; Padfield et al., 2006a,b, 2008).”
Automated subcellular location determination and high-throughput microscopy. (2007, methodology): “These include using parametric and geometric active contours (Coulot et al., 2006; Dufour et al., 2005; Zimmer et al., 2002), a combined filtering and watershed algorithm (Adiga et al.”
On the digital trail of mobile cells (2006, methodology): “Such an essentially 2-D method does not, however, allow the direct incorporation of 3-D constraints, such as smoothness, volume, or shape, which are useful to improve segmentation of noisy images [1], [12], and [27].”
Advanced Level-Set-Based Cell Tracking in Time-Lapse Fluorescence Microscopy (2010, methodology): “Applying to (5) the Euler–Lagrange equation, we obtain the mean values and for each level-set function (for analytical expressions see [ 35 ]) and the equivalent of the evolution (4)”
Automated Cell Lineage Construction: A Rapid Method to Analyze Clonal Development Established with Murine Neural Progenitor Cells (2006, methodology): “23 Level set methods 24,25 are able to handle topology changes due to cell division; however, deciding which cell is the parent of each child would still be an issue with such methods.”
Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review (2016, methodology): “[189] have presented an advanced level set based cell segmentation and tracking framework by introducing a number of improvements on the coupled-active-surfaces framework [226] including an efficient stopping criterion, energy minimization without partial”
Generation of digital phantoms of cell nuclei and simulation of image formation in 3D image cytometry (2009, background): “In optical microscopy, great progress in simulating image data has been made mainly during the past 3 years, during which several papers (20,23,24,33) have given straightforward recipes or even offered useful software toolboxes.”
Automated and semi‐automated cell tracking: addressing portability challenges (2011, methodology): “Dufour et al. (2005) and Dzyubachyk et al. (2010) use active contours and level-set based methods.”
Visualization of image data from cells to organisms (2010, neutral): “Often these studies require reliable tracking algorithms 12,13 that enable researchers to follow the same object (for example, single molecules or cells) over time and to extract and visualize trajectories and other measurements (for example, color-coded speed of cells in a developing embryo 14 ).”
Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan–Vese Model (2013, methodology): “In contrast to [18], [20], [21], we minimize the original Chan–Vese model [30] in the fast level set-like (FLS) [32] and graph cut (GC) [33] frameworks without solving any PDE, and replace coupling of multiple separate models with a topological prior that exploits the object indication function [34]”
Icy: an open bioimage informatics platform for extended reproducible research (2012, background): “The active contours (two dimensions) 23 and active meshes (three dimensions) 24,25 plug-ins are found in protocols dedicated to segmenting and tracking large, deformable objects (typically cells or nuclei) for studying cell-cell interactions in the immune system 26 , and the morphology and motility…”
Segmentation of Clustered Nuclei With Shape Markers and Marking Function (2009, methodology): “The approach has been used for segmenting and tracking cells in 2-D images [5] and dynamics of 3-D images [6].”