# IonMorphNet: Generalizable Learning of Ion Image Morphologies for Peak Picking in Mass Spectrometry Imaging

arXiv: https://arxiv.org/abs/2604.19369 · HTML: https://mlsanity.com/paper/2604.19369/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 45 references that are in the map.
- First posted on arXiv 21 Apr 2026.

## Builds on (most cited first, 18 of 18)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features](https://mlsanity.com/paper/1905.04899/) (2019)
- [Xception: Deep Learning with Depthwise Separable Convolutions](https://mlsanity.com/paper/1610.02357/) (2016)
- [Improved Regularization of Convolutional Neural Networks with Cutout](https://mlsanity.com/paper/1708.04552/) (2017)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Swin Transformer V2: Scaling Up Capacity and Resolution](https://mlsanity.com/paper/2111.09883/) (2021)
- [PVT v2: Improved Baselines with Pyramid Vision Transformer](https://mlsanity.com/paper/2106.13797/) (2021)
- [ConvNeXt V2: Co-designing and Scaling ConvNets with Masked Autoencoders](https://mlsanity.com/paper/2301.00808/) (2023)
- [Deep Learning for Tumor Classification in Imaging Mass Spectrometry](https://mlsanity.com/paper/1705.01015/) (2017)
- [Peak detection for MALDI mass spectrometry imaging data using sparse frame multipliers](https://mlsanity.com/paper/1911.00491/) (2019)
- [Hyperspectral Benchmark: Bridging the Gap between HSI Applications through Comprehensive Dataset and Pretraining](https://mlsanity.com/paper/2309.11122/) (2023)
- [Spatial self-supervised Peak Learning and correlation-based Evaluation of peak picking in Mass Spectrometry Imaging](https://mlsanity.com/paper/2603.10487/) (2026)

## Abstract (arXiv)

Peak picking is a fundamental preprocessing step in Mass Spectrometry Imaging (MSI), where each sample is represented by hundreds to thousands of ion images. Existing approaches require careful dataset-specific hyperparameter tuning, and often fail to generalize across acquisition protocols. We introduce IonMorphNet, a spatial-structure-aware representation model for ion images that enables fully data-driven peak picking without any task-specific supervision. We curate 53 publicly available MSI datasets and define six structural classes capturing representative spatial patterns in ion images to train standard image backbones for structural pattern classification. Once trained, IonMorphNet can assess ion images and perform peak picking without additional hyperparameter tuning. Using a ConvNeXt V2-Tiny backbone, our approach improves peak picking performance by +7 % mSCF1 compared to state-of-the-art methods across multiple datasets. Beyond peak picking, we demonstrate that spatially informed channel reduction enables a 3D CNN for patch-based tumor classification in MSI. This approach matches or exceeds pixel-wise spectral classifiers by up to +7.3 % Balanced Accuracy on three tumor classification tasks, indicating meaningful ion image selection. The source code and model weights are available at https://github.com/CeMOS-IS/IonMorphNet.