Tracking living cells in video sequence is difficult, because of cell morphology and high similarities between cells. Tracking-by-detection methods are widely used in multi-cell tracking. We perform multi-cell tracking based on the cell centroid detection, and the performance of the detector has high impact on tracking performance. In this paper, UNet is utilized to extract inter-frame and intra-frame spatio-temporal information of cells. Detection performance of cells in mitotic phase is improved by multi-frame input. Good detection results facilitate multi-cell tracking. A mitosis detection algorithm is proposed to detect cell mitosis and the cell lineage is built up. Another UNet is utilized to acquire primary segmentation. Jointly using detection and primary segmentation, cells can be fine segmented in highly dense cell population. Experiments are conducted to evaluate the effectiveness of our method, and results show its state-of-the-art performance.
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 from all detected events not only to reconstruct the dynamic evolution of the radionuclide distribution, but also to improve the reconstruction at each single time point by enforcing temporal consistency. This is achieved via optimal transport regularization where in principle, among all possible temporally evolving radionuclide distributions consistent with the PET measurement, the one is chosen with least kinetic motion energy. The reconstruction is found by convex optimization so that there is no dependence on the initialization of the method. We study its behaviour on simulated data of a human PET system and demonstrate its robustness even in settings with very low radioactivity. In contrast to previously reported cell tracking algorithms, our technique is oblivious to the number of tracked cells. Without any additional complexity one or multiple cells can be reconstructed, and the model automatically determines the number of particles. For instance, four radiolabelled cells moving at a velocity of 3.1 mm/s and a PET recorded count rate of 1.1 cps (for each cell) could be simultaneously tracked with a tracking accuracy of 5.3 mm inside a simulated human body.
There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .
We propose a novel approach to automatically tracking cell populations in time-lapse images. To account for cell occlusions and overlaps, we introduce a robust method that generates an over-complete set of competing detection hypotheses. We then perform detection and tracking simultaneously on these hypotheses by solving to optimality an integer program with only one type of flow variables. This eliminates the need for heuristics to handle missed detections due to occlusions and complex morphology. We demonstrate the effectiveness of our approach on a range of challenging sequences consisting of clumped cells and show that it outperforms state-of-the-art techniques.
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. Data types to which the method is applicable are characterized as follows: (i) cells are imaged as globular-like objects, (ii) it is difficult to distinguish cells based only on shape and size, (iii) the number of imaged cells ranges in several hundreds, (iv) moves of nearly-located cells are strongly correlated and (v) cells do not divide. We developed a tracking software suite which we call SPF-CellTracker. Incorporating dependency on cells' moves into prediction model is the key to reduce the tracking errors: cell-switching and coalescence of tracked positions. We model target cells' correlated moves as a Markov random field and we also derive a fast computation algorithm, which we call spatial particle filter. With the live-imaging data of nuclei of C. elegans neurons in which approximately 120 nuclei of neurons are imaged, we demonstrate an advantage of the proposed method over the standard particle filter and a method developed by Tokunaga et al. (2014).
Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid growth in the amount of image data being captured. To efficiently and reliably extract useful insights from these captured sequences, automated cell tracking is essential. This is a challenging problem due to large variation in the appearance and shapes of cells depending on many factors including imaging methodology, biological characteristics of cells, cell matrix composition, labeling methodology, etc. Often cell tracking methods require a sequence-specific segmentation method and manual tuning of many tracking parameters, which limits their applicability to sequences other than those they are designed for. In this paper, we propose 1) a deep learning based cell proposal method, which proposes candidates for cells along with their scores, and 2) a cell tracking method, which links proposals in adjacent frames in a graphical model using edges representing different cellular events and poses joint cell detection and tracking as the selection of a subset of cell and edge proposals. Our method is completely automated and given enough training data can be applied to a wide variety of microscopy sequences. We evaluate our method on multiple fluorescence and phase contrast microscopy sequences containing cells of various shapes and appearances from ISBI cell tracking challenge, and show that our method outperforms existing cell tracking methods. Code is available at: https://github.com/SaadUllahAkram/CellTracker
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 time-lapse movies. Our method is based on a dynamic neighborhoods formation and matching approach, inspired by motion estimation algorithms for video compression. Moreover, it exploits "divide and conquer" opportunities to solve effectively the challenging cells tracking problem in overcrowded bacterial colonies. Using cell movies generated by different labs we demonstrate that the accuracy of the proposed method remains very high (exceeds 97%) even when analyzing large overcrowded microbial colonies.
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to analyze successfully complex cell movies, imaging multiple interacting bacterial clones as they grow and merge to generate overcrowded bacterial communities with thousands of cells in the field of view, segmentation results should be near perfect to warrant good tracking results. We introduce here a fully automated closed-loop bio-inspired computational strategy that exploits prior knowledge about the expected structure of a colony's lineage tree to locate and correct segmentation errors in analyzed movie frames. We show that this correction strategy is effective, resulting in improved cell tracking and consequently trustworthy deep colony lineage trees. Our image analysis approach has the unique capability to keep tracking cells even after clonal subpopulations merge in the movie. This enables the reconstruction of the complete Forest of Lineage Trees (FLT) representation of evolving multi-clonal bacterial communities. Moreover, the percentage of valid cell trajectories extracted from the image analysis almost doubles after segmentation correction. This plethora of trustworthy data extracted from a complex cell movie analysis enables single-cell analytics as a tool for addressing compelling questions for human health, such as understanding the role of single-cell stochasticity in antibiotics resistance without losing site of the inter-cellular interactions and microenvironment effects that may shape it.
Live cell microscopy sequences exhibit complex spatial structures and complicated temporal behaviour, making their analysis a challenging task. Considering cell segmentation problem, which plays a significant role in the analysis, the spatial properties of the data can be captured using Convolutional Neural Networks (CNNs). Recent approaches show promising segmentation results using convolutional encoder-decoders such as the U-Net. Nevertheless, these methods are limited by their inability to incorporate temporal information, that can facilitate segmentation of individual touching cells or of cells that are partially visible. In order to exploit cell dynamics we propose a novel segmentation architecture which integrates Convolutional Long Short Term Memory (C-LSTM) with the U-Net. The network's unique architecture allows it to capture multi-scale, compact, spatio-temporal encoding in the C-LSTMs memory units. The method was evaluated on the Cell Tracking Challenge and achieved state-of-the-art results (1st on Fluo-N2DH-SIM+ and 2nd on DIC-C2DL-HeLa datasets) The code is freely available at: https://github.com/arbellea/LSTM-UNet.git