# Tera-MIND: Tera-scale mouse brain simulation via spatial mRNA-guided diffusion

arXiv: https://arxiv.org/abs/2503.01220 · HTML: https://mlsanity.com/paper/2503.01220/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 16 of its 55 references that are in the map.
- First posted on arXiv 3 Mar 2025.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 16 of 16)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [Open-Sora: Democratizing Efficient Video Production for All](https://mlsanity.com/paper/2412.20404/) (2024)
- [Movie Gen: A Cast of Media Foundation Models](https://mlsanity.com/paper/2410.13720/) (2024)
- [Scaling up GANs for Text-to-Image Synthesis](https://mlsanity.com/paper/2303.05511/) (2023)
- [Generating Images with Sparse Representations](https://mlsanity.com/paper/2103.03841/) (2021)
- [A Survey on Generative Diffusion Model](https://mlsanity.com/paper/2209.02646/) (2022)
- [Positional Encoding as Spatial Inductive Bias in GANs](https://mlsanity.com/paper/2012.05217/) (2020)
- [COCO-GAN: Generation by Parts via Conditional Coordinating](https://mlsanity.com/paper/1904.00284/) (2019)
- [InfinityGAN: Towards Infinite-Pixel Image Synthesis](https://mlsanity.com/paper/2104.03963/) (2021)
- [SinFusion: Training Diffusion Models on a Single Image or Video](https://mlsanity.com/paper/2211.11743/) (2022)
- [Patched Denoising Diffusion Models For High-Resolution Image Synthesis](https://mlsanity.com/paper/2308.01316/) (2023)
- [The Dawn of Video Generation: Preliminary Explorations with SORA-like Models](https://mlsanity.com/paper/2410.05227/) (2024)

## Abstract (arXiv)

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Using emerging tissue profiling technologies, researchers charted comprehensive atlases of mammalian brain with sub-cellular resolution and spatially resolved transcriptomic data. However, these tera-scale volumetric atlases pose computational challenges for modeling intricate brain structures within the native spatial context. We propose Tera-MIND, a novel generative framework capable of simulating Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial gene expression as conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D textitgene-textitgene self-attention, we identify spatial molecular interactions for key transcriptomic pathways, including glutamatergic and dopaminergic neuronal systems. Lastly, we showcase the translational applicability of Tera-MIND on previously unseen human brain samples. Tera-MIND offers an efficient generative modeling of whole virtual organisms, paving the way for integrative applications in biomedical research. Project website: https://musikisomorphie.github.io/Tera-MIND.html