Hari Shroff

Andrew Lauziere, Ryan Christensen, Hari Shroff

The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using fluorescence microscopy images. However, established methods to track cells in late-stage development fail to generalize once sporadic muscular twitching has begun. We build upon methodology which uses skin cells as fiducial markers to carry out cell tracking despite random twitching. In particular, we present a cell nucleus segmentation and tracking procedure which was integrated into a 3D rendering GUI to improve efficiency in tracking cells across late-stage development. Results on images depicting aforementioned muscle cell nuclei across three test embryos suggest the fiducial markers in conjunction with a classic tracking paradigm overcome sporadic twitching.

Magdalena C. Schneider, Courtney Johnson, Cedric Allier et al.

Sample-induced aberrations and optical imperfections limit the resolution of fluorescence microscopy. Phase diversity is a powerful technique that leverages complementary phase information in sequentially acquired images with deliberately introduced aberrations--the phase diversities--to enable phase and object reconstruction and restore diffraction-limited resolution. These phase diversities are typically introduced into the optical path via a deformable mirror. Existing phase-diversity-based methods are limited to Zernike modes, require large numbers of diversity images, or depend on accurate mirror calibration--which are all suboptimal. We present DeepPD, a deep learning-based framework that combines neural representations of the object and wavefront with a learned model of the deformable mirror to jointly estimate both object and phase from only five images. DeepPD improves robustness and reconstruction quality over previous approaches, even under severe aberrations. We demonstrate its performance on calibration targets and biological samples, including immunolabeled myosin in fixed PtK2 cells.

Baiyang Dai, Jiamin Yang, Hari Shroff et al.

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early $\textit{C. elegans}$ embryogenesis using machine learning. Cell identification during $\textit{C. elegans}$ embryogenesis would provide insights into neural development with implications for higher organisms including humans. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 91%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in time-lapse imaging sequences directly from simple spatio-temporal features.

Andrew Lauziere, Evan Ardiel, Stephen Xu et al.

Current methods in multiple object tracking (MOT) rely on independent object trajectories undergoing predictable motion to effectively track large numbers of objects. Adversarial conditions such as volatile object motion and imperfect detections create a challenging tracking landscape in which established methods may yield inadequate results. Multiple hypothesis hypergraph tracking (MHHT) is developed to perform MOT among interdependent objects amid noisy detections. The method extends traditional multiple hypothesis tracking (MHT) via hypergraphs to model correlated object motion, allowing for robust tracking in challenging scenarios. MHHT is applied to perform seam cell tracking during late-stage embryogenesis in embryonic C. elegans.

Andrew Lauziere, Ryan Christensen, Hari Shroff et al.

Finding an optimal correspondence between point sets is a common task in computer vision. Existing techniques assume relatively simple relationships among points and do not guarantee an optimal match. We introduce an algorithm capable of exactly solving point set matching by modeling the task as hypergraph matching. The algorithm extends the classical branch and bound paradigm to select and aggregate vertices under a proposed decomposition of the multilinear objective function. The methodology is motivated by Caenorhabditis elegans, a model organism used frequently in developmental biology and neurobiology. The embryonic C. elegans contains seam cells that can act as fiducial markers allowing the identification of other nuclei during embryo development. The proposed algorithm identifies seam cells more accurately than established point-set matching methods, while providing a framework to approach other similarly complex point set matching tasks.