An Ant Colony Inspired Multi-Bernoulli Filter for Cell Tracking in Time-Lapse Microscopy Sequences

2020 ◽  
Vol 24 (6) ◽  
pp. 1703-1716 ◽  
Author(s):  
Benlian Xu ◽  
Mingli Lu ◽  
Jinliang Cong ◽  
Brett D. Nener
2021 ◽  
Vol 12 ◽  
Author(s):  
Florent Lemaître ◽  
Ana Carmena Moratalla ◽  
Negar Farzam-kia ◽  
Yves Carpentier Solorio ◽  
Olivier Tastet ◽  
...  

To fully perform their functions, T lymphocytes migrate within organs’ parenchyma and interact with local cells. Infiltration of T lymphocytes within the central nervous system (CNS) is associated with numerous neurodegenerative disorders. Nevertheless, how these immune cells communicate and respond to neural cells remains unresolved. To investigate the behavior of T lymphocytes that reach the CNS, we have established an in vitro co-culture model and analyzed the spatiotemporal interactions between human activated CD8+ T lymphocytes and primary human astrocytes and neurons using time-lapse microscopy. By combining multiple variables extracted from individual CD8+ T cell tracking, we show that CD8+ T lymphocytes adopt a more motile and exploratory behavior upon interacting with astrocytes than with neurons. Pretreatment of astrocytes or neurons with IL-1β to mimic in vivo inflammation significantly increases CD8+ T lymphocyte motility. Using visual interpretation and analysis of numerical variables extracted from CD8+ T cell tracking, we identified four distinct CD8+ T lymphocyte behaviors: scanning, dancing, poking and round. IL-1β-pretreatment significantly increases the proportion of scanning CD8+ T lymphocytes, which are characterized by active exploration, and reduces the proportion of round CD8+ T lymphocytes, which are less active. Blocking MHC class I on astrocytes significantly diminishes the proportion of poking CD8+ T lymphocytes, which exhibit synapse-like interactions. Lastly, our co-culture time-lapse model is easily adaptable and sufficiently sensitive and powerful to characterize and quantify spatiotemporal interactions between human T lymphocytes and primary human cells in different conditions while preserving viability of fragile cells such as neurons and astrocytes.


Cell Reports ◽  
2020 ◽  
Vol 32 (5) ◽  
pp. 107984
Author(s):  
Chengzhe Tian ◽  
Chen Yang ◽  
Sabrina L. Spencer

2011 ◽  
Vol 20 (7) ◽  
pp. 1925-1937 ◽  
Author(s):  
A Dufour ◽  
R Thibeaux ◽  
E Labruyere ◽  
N Guillen ◽  
J-C Olivo-Marin

Author(s):  
Chengzhe Tian ◽  
Chen Yang ◽  
Sabrina L. Spencer

SummaryTime-lapse microscopy provides an unprecedented opportunity to monitor single-cell dynamics. However, tracking cells for long periods of time remains a technical challenge, especially for multi-day, large-scale movies with rapid cell migration, high cell density, and drug treatments that alter cell morphology/behavior. Here, we present EllipTrack, a global-local cell-tracking pipeline optimized for tracking such movies. EllipTrack first implements a global track-linking algorithm to construct tracks that maximize the probability of cell lineages, and then corrects tracking mistakes with a local track-correction module where tracks generated by the global algorithm are systematically examined and amended if a more probable alternative can be found. Through benchmarking, we show that EllipTrack outperforms state-of-the-art cell trackers and generates nearly error-free cell lineages for multiple large-scale movies. In addition, EllipTrack can adapt to time- and cell density-dependent changes in cell migration speeds, requires minimal training datasets, and provides a user-friendly interface. EllipTrack is available at github.com/tianchengzhe/EllipTrack.


2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Dai Fei Elmer Ker ◽  
Sungeun Eom ◽  
Sho Sanami ◽  
Ryoma Bise ◽  
Corinne Pascale ◽  
...  

2020 ◽  
pp. 47-50
Author(s):  
N. V. Saraeva ◽  
N. V. Spiridonova ◽  
M. T. Tugushev ◽  
O. V. Shurygina ◽  
A. I. Sinitsyna

In order to increase the pregnancy rate in the assisted reproductive technology, the selection of one embryo with the highest implantation potential it is very important. Time-lapse microscopy (TLM) is a tool for selecting quality embryos for transfer. This study aimed to assess the benefits of single-embryo transfer of autologous oocytes performed on day 5 of embryo incubation in a TLM-equipped system in IVF and ICSI programs. Single-embryo transfer following incubation in a TLM-equipped incubator was performed in 282 patients, who formed the main group; the control group consisted of 461 patients undergoing single-embryo transfer following a traditional culture and embryo selection procedure. We assessed the quality of transferred embryos, the rates of clinical pregnancy and delivery. The groups did not differ in the ratio of IVF and ICSI cycles, average age, and infertility factor. The proportion of excellent quality embryos for transfer was 77.0% in the main group and 65.1% in the control group (p = 0.001). In the subgroup with receiving eight and less oocytes we noted the tendency of receiving more quality embryos in the main group (р = 0.052). In the subgroup of nine and more oocytes the quality of the transferred embryos did not differ between two groups. The clinical pregnancy rate was 60.2% in the main group and 52.9% in the control group (p = 0.057). The delivery rate was 45.0% in the main group and 39.9% in the control group (p > 0.050).


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