# Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens

arXiv: https://arxiv.org/abs/2503.12593 · HTML: https://mlsanity.com/paper/2503.12593/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 40 references that are in the map.
- First posted on arXiv 16 Mar 2025.

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

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [ViViT: A Video Vision Transformer](https://mlsanity.com/paper/2103.15691/) (2021)
- [Deep Networks with Stochastic Depth](https://mlsanity.com/paper/1603.09382/) (2016)
- [Multiscale Vision Transformers](https://mlsanity.com/paper/2104.11227/) (2021)
- [MViTv2: Improved Multiscale Vision Transformers for Classification and Detection](https://mlsanity.com/paper/2112.01526/) (2021)
- [Hiera: A Hierarchical Vision Transformer without the Bells-and-Whistles](https://mlsanity.com/paper/2306.00989/) (2023)
- [Coordinate-based neural representations for computational adaptive optics in widefield microscopy](https://mlsanity.com/paper/2307.03812/) (2023)
- [Universal adaptive optics for microscopy through embedded neural network control](https://mlsanity.com/paper/2301.02647/) (2023)

## Abstract (arXiv)

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. While wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement, and slow when serially mapping spatially varying aberrations across large fields of view. Here, we introduce AOViFT (Adaptive Optical Vision Fourier Transformer) -- a machine learning-based aberration sensing framework built around a 3D multistage Vision Transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time, and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or post-acquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.