# SHREC 2021: Classification in cryo-electron tomograms

arXiv: https://arxiv.org/abs/2203.10035 · HTML: https://mlsanity.com/paper/2203.10035/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 40 references that are in the map.
- First posted on arXiv 18 Mar 2022.

## Builds on (most cited first, 17 of 17)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (2016)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting](https://mlsanity.com/paper/1506.04214/) (2015)
- [Beyond a Gaussian Denoiser: Residual Learning of Deep CNN for Image Denoising](https://mlsanity.com/paper/1608.03981/) (2016)
- [Multi-Scale Context Aggregation by Dilated Convolutions](https://mlsanity.com/paper/1511.07122/) (2015)
- [Focal Loss for Dense Object Detection](https://mlsanity.com/paper/1708.02002/) (2017)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [Learning Spatio-Temporal Features with 3D Residual Networks for Action Recognition](https://mlsanity.com/paper/1708.07632/) (2017)
- [DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM](https://mlsanity.com/paper/1605.01838/) (2016)
- [CFCM: Segmentation via Coarse to Fine Context Memory](https://mlsanity.com/paper/1806.01413/) (2018)
- [Deeply Cascaded U-Net for Multi-Task Image Processing](https://mlsanity.com/paper/2005.00225/) (2020)

## Built on by (most cited first, 5 of 5)

- [FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer](https://mlsanity.com/paper/2304.02011/) (2023)
- [Affinity-VAE: incorporating prior knowledge in representation learning from scientific images](https://mlsanity.com/paper/2209.04517/) (2022)
- [Tensorial template matching for fast cross-correlation with rotations and its application for tomography](https://mlsanity.com/paper/2408.02398/) (2024)
- [CryoCCD: Conditional Cycle-consistent Diffusion with Biophysical Modeling for Cryo-EM Synthesis](https://mlsanity.com/paper/2505.23444/) (2025)
- [SaSi: A Self-augmented and Self-interpreted Deep Learning Approach for Few-shot Cryo-ET Particle Detection](https://mlsanity.com/paper/2505.19948/) (2025)

## Abstract (arXiv)

Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and inability to obtain images from all angles. Computational methods are key to analyze cryo-electron tomograms. To promote innovation in computational methods, we generate a novel simulated dataset to benchmark different methods of localization and classification of biological macromolecules in tomograms. Our publicly available dataset contains ten tomographic reconstructions of simulated cell-like volumes. Each volume contains twelve different types of complexes, varying in size, function and structure. In this paper, we have evaluated seven different methods of finding and classifying proteins. Seven research groups present results obtained with learning-based methods and trained on the simulated dataset, as well as a baseline template matching (TM), a traditional method widely used in cryo-ET research. We show that learning-based approaches can achieve notably better localization and classification performance than TM. We also experimentally confirm that there is a negative relationship between particle size and performance for all methods.