# ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

arXiv: https://arxiv.org/abs/2404.19665 · HTML: https://mlsanity.com/paper/2404.19665/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 51 references that are in the map.
- First posted on arXiv 30 Apr 2024.

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

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances](https://mlsanity.com/paper/1306.0895/) (2013)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [fastMRI: An Open Dataset and Benchmarks for Accelerated MRI](https://mlsanity.com/paper/1811.08839/) (2018)
- [MoDL: Model Based Deep Learning Architecture for Inverse Problems](https://mlsanity.com/paper/1712.02862/) (2017)
- [Learning a Variational Network for Reconstruction of Accelerated MRI Data](https://mlsanity.com/paper/1704.00447/) (2017)
- [Learned Primal-dual Reconstruction](https://mlsanity.com/paper/1707.06474/) (2017)
- [NeMo: a toolkit for building AI applications using Neural Modules](https://mlsanity.com/paper/1909.09577/) (2019)
- [A Deep Cascade of Convolutional Neural Networks for Dynamic MR Image Reconstruction](https://mlsanity.com/paper/1704.02422/) (2017)
- [End-to-End Variational Networks for Accelerated MRI Reconstruction](https://mlsanity.com/paper/2004.06688/) (2020)
- [TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning](https://mlsanity.com/paper/2003.04696/) (2020)
- [ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset](https://mlsanity.com/paper/2206.06694/) (2022)
- [Convolutional Recurrent Neural Networks for Dynamic MR Image Reconstruction](https://mlsanity.com/paper/1712.01751/) (2017)
- [NiftyNet: a deep-learning platform for medical imaging](https://mlsanity.com/paper/1709.03485/) (2017)
- [SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation](https://mlsanity.com/paper/2203.06823/) (2022)
- [Recurrent Variational Network: A Deep Learning Inverse Problem Solver applied to the task of Accelerated MRI Reconstruction](https://mlsanity.com/paper/2111.09639/) (2021)
- [VS-Net: Variable splitting network for accelerated parallel MRI reconstruction](https://mlsanity.com/paper/1907.10033/) (2019)
- [Joint CS-MRI Reconstruction and Segmentation with a Unified Deep Network](https://mlsanity.com/paper/1805.02165/) (2018)
- [Multi-Coil MRI Reconstruction Challenge -- Assessing Brain MRI Reconstruction Models and their Generalizability to Varying Coil Configurations](https://mlsanity.com/paper/2011.07952/) (2020)
- [Task adapted reconstruction for inverse problems](https://mlsanity.com/paper/1809.00948/) (2018)
- [PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation](https://mlsanity.com/paper/2208.09350/) (2022)
- [Deep, Deep Learning with BART](https://mlsanity.com/paper/2202.14005/) (2022)
- [Assessment of Data Consistency through Cascades of Independently Recurrent Inference Machines for fast and robust accelerated MRI reconstruction](https://mlsanity.com/paper/2111.15498/) (2021)
- [Reconstruction and Segmentation of Parallel MR Data using Image Domain DEEP-SLR](https://mlsanity.com/paper/2102.01172/) (2021)

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

- [Anatomy-Guided Representation Learning Using a Transformer-Based Network for Thyroid Nodule Segmentation in Ultrasound Images](https://mlsanity.com/paper/2512.12662/) (2025)

## Abstract (arXiv)

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.