# DynaCLR: Contrastive Learning of Cellular Dynamics with Temporal Regularization

arXiv: https://arxiv.org/abs/2410.11281 · HTML: https://mlsanity.com/paper/2410.11281/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 47 references that are in the map.
- First posted on arXiv 15 Oct 2024.

## Builds on (most cited first, 14 of 14)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Visualizing and Understanding Convolutional Networks](https://mlsanity.com/paper/1311.2901/) (2013)
- [Captum: A unified and generic model interpretability library for PyTorch](https://mlsanity.com/paper/2009.07896/) (2020)
- [Time-Contrastive Networks: Self-Supervised Learning from Video](https://mlsanity.com/paper/1704.06888/) (2017)
- [Spatiotemporal Contrastive Video Representation Learning](https://mlsanity.com/paper/2008.03800/) (2020)
- [Unsupervised Learning of Disentangled Representations from Video](https://mlsanity.com/paper/1705.10915/) (2017)
- [TCLR: Temporal Contrastive Learning for Video Representation](https://mlsanity.com/paper/2101.07974/) (2021)
- [A Contrastive Learning Approach for Training Variational Autoencoder Priors](https://mlsanity.com/paper/2010.02917/) (2020)
- [Masked Autoencoders are Scalable Learners of Cellular Morphology](https://mlsanity.com/paper/2309.16064/) (2023)
- [Self-supervised dense representation learning for live-cell microscopy with time arrow prediction](https://mlsanity.com/paper/2305.05511/) (2023)

## Built on by (most cited first, 2 of 2)

- [WaveOrder: A differentiable wave-optical framework for scalable biological microscopy with diverse modalities](https://mlsanity.com/paper/2412.09775/) (2024)
- [Unsupervised Learning of Cell Instances with Generative Routing Pyramids](https://mlsanity.com/paper/2608.16810/) (2026)

## Abstract (arXiv)

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.