# Cross-Subject Modeling for Widefield Calcium Imaging via Atlas-Aligned Spatiotemporal Tokenization

arXiv: https://arxiv.org/abs/2607.09754 · HTML: https://mlsanity.com/paper/2607.09754/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 59 references that are in the map.
- First posted on arXiv 5 Jul 2026.

## Builds on (most cited first, 25 of 25)

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- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [Revisiting Feature Prediction for Learning Visual Representations from Video](https://mlsanity.com/paper/2404.08471/) (2024)
- [Learnable latent embeddings for joint behavioral and neural analysis](https://mlsanity.com/paper/2204.00673/) (2022)
- [BrainBERT: Self-supervised representation learning for intracranial recordings](https://mlsanity.com/paper/2302.14367/) (2023)
- [Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Masking](https://mlsanity.com/paper/2409.19407/) (2024)
- [A Unified, Scalable Framework for Neural Population Decoding](https://mlsanity.com/paper/2310.16046/) (2023)
- [Towards a "universal translator" for neural dynamics at single-cell, single-spike resolution](https://mlsanity.com/paper/2407.14668/) (2024)
- [Population Transformer: Learning Population-level Representations of Neural Activity](https://mlsanity.com/paper/2406.03044/) (2024)
- [Neural Encoding and Decoding at Scale](https://mlsanity.com/paper/2504.08201/) (2025)
- [Neural decoding from stereotactic EEG: accounting for electrode variability across subjects](https://mlsanity.com/paper/2411.10458/) (2024)
- [Challenges for machine learning in clinical translation of big data imaging studies](https://mlsanity.com/paper/2107.05630/) (2021)
- [Du-IN: Discrete units-guided mask modeling for decoding speech from Intracranial Neural signals](https://mlsanity.com/paper/2405.11459/) (2024)
- [Exploring Behavior-Relevant and Disentangled Neural Dynamics with Generative Diffusion Models](https://mlsanity.com/paper/2410.09614/) (2024)
- [BRAID: Input-Driven Nonlinear Dynamical Modeling of Neural-Behavioral Data](https://mlsanity.com/paper/2509.18627/) (2025)
- [BaRISTA: Brain Scale Informed Spatiotemporal Representation of Human Intracranial Neural Activity](https://mlsanity.com/paper/2512.12135/) (2025)
- [Dynamical Modeling of Behaviorally Relevant Spatiotemporal Patterns in Neural Imaging Data](https://mlsanity.com/paper/2509.18507/) (2025)
- [Cross-Modal Representational Knowledge Distillation for Enhanced Spike-Informed LFP Modeling](https://mlsanity.com/paper/2512.12461/) (2025)
- [Dynamical modeling of nonlinear latent factors in multiscale neural activity with real-time inference](https://mlsanity.com/paper/2512.12462/) (2025)
- [Chronic, cortex-wide imaging of specific cell populations during behavior](https://mlsanity.com/paper/2010.15191/) (2020)

## Built on by (most cited first, 1 of 1)

- [A Low-Power Wearable Respiratory Sensor for Non-Invasive Stress Monitoring](https://mlsanity.com/paper/2608.05697/) (2026)

## Abstract (arXiv)

Large-scale, multi-subject widefield calcium imaging provides unprecedented access to brain-wide cortical dynamics. However, the high dimensionality, complex spatiotemporal structure, and substantial task-irrelevant activity in widefield recordings have largely restricted modeling efforts to single-session analyses, limiting scalability and generalization. While multi-subject pretrained models have been explored for some neural modalities, multi-subject models for widefield calcium imaging have not yet been demonstrated; further, subject-invariant zero-shot behavior decoding remains elusive for multi-subject models across neural modalities more broadly. As a first step toward foundation modeling of widefield data, we introduce WiCAT, a multi-subject model that leverages self-supervised pretraining to both outperform single-session models and enable zero-shot behavior decoding on unseen subjects. WiCAT introduces an atlas-grounded tokenization scheme without session-specific components and learns globally shared spatiotemporal representations. Across multiple widefield datasets, the pretrained model supports lightweight downstream decoding, transfers across subjects, tasks, and datasets, and outperforms baseline models. Notably, the model also achieves robust zero-shot continuous behavior decoding and left-out brain region reconstruction on unseen subjects.