Spatial-Temporal Mitosis Detection in Phase-Contrast Microscopy via Likelihood Map Estimation by 3DCNN

Automated mitotic detection in time-lapse phasecontrast microscopy provides us much information for cell behavior analysis, and thus several mitosis detection methods have been proposed. However, these methods still have two problems; 1) they cannot detect multiple mitosis events when there are closely placed. 2) they do not consider the annotation gaps, which may occur since the appearances of mitosis cells are very similar before and after the annotated frame. In this paper, we propose a novel mitosis detection method that can detect multiple mitosis events in a candidate sequence and mitigate the human annotation gap via estimating a spatiotemporal likelihood map by 3DCNN. In this training, the loss gradually decreases with the gap size between ground truth and estimation. This mitigates the annotation gaps. Our method outperformed the compared methods in terms of F1- score using a challenging dataset that contains the data under four different conditions.Comment: 5 pages, 6 figures, Accepted in EMBC 202

An unsupervised long short-term memory neural network for event detection in cell videos

We propose an automatic unsupervised cell event detection and classification method, which expands convolutional Long Short-Term Memory (LSTM) neural networks, for cellular events in cell video sequences. Cells in images that are captured from various biomedical applications usually have different shapes and motility, which pose difficulties for the automated event detection in cell videos. Current methods to detect cellular events are based on supervised machine learning and rely on tedious manual annotation from investigators with specific expertise. So that our LSTM network could be trained in an unsupervised manner, we designed it with a branched structure where one branch learns the frequent, regular appearance and movements of objects and the second learns the stochastic events, which occur rarely and without warning in a cell video sequence. We tested our network on a publicly available dataset of densely packed stem cell phase-contrast microscopy images undergoing cell division. This dataset is considered to be more challenging that a dataset with sparse cells. We compared our method to several published supervised methods evaluated on the same dataset and to a supervised LSTM method with a similar design and configuration to our unsupervised method. We used an F1-score, which is a balanced measure for both precision and recall. Our results show that our unsupervised method has a higher or similar F1-score when compared to two fully supervised methods that are based on Hidden Conditional Random Fields (HCRF), and has comparable accuracy with the current best supervised HCRF-based method. Our method was generalizable as after being trained on one video it could be applied to videos where the cells were in different conditions. The accuracy of our unsupervised method approached that of its supervised counterpart

Semi-supervised estimation of event temporal length for cell event detection

Cell event detection in cell videos is essential for monitoring of cellular behavior over extended time periods. Deep learning methods have shown great success in the detection of cell events for their ability to capture more discriminative features of cellular processes compared to traditional methods. In particular, convolutional long short-term memory (LSTM) models, which exploits the changes in cell events observable in video sequences, is the state-of-the-art for mitosis detection in cell videos. However, their limitations are the determination of the input sequence length, which is often performed empirically, and the need for a large annotated training dataset which is expensive to prepare. We propose a novel semi-supervised method of optimal length detection for mitosis detection with two key contributions: (i) an unsupervised step for learning the spatial and temporal locations of cells in their normal stage and approximating the distribution of temporal lengths of cell events and, (ii) a step of inferring, from that distribution, an optimal input sequence length and a minimal number of annotated frames for training a LSTM model for each particular video. We evaluated our method in detecting mitosis in densely packed stem cells in a phase-contrast microscopy videos. Our experimental data prove that increasing the input sequence length of LSTM can lead to a decrease in performance. Our results also show that by approximating the optimal input sequence length of the tested video, a model trained with only 18 annotated frames achieved F1-scores of 0.880-0.907, which are 10% higher than those of other published methods with a full set of 110 training annotated frames