# A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

arXiv: https://arxiv.org/abs/1706.04970 · HTML: https://mlsanity.com/paper/1706.04970/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 15 Jun 2017.

## Built on by (most cited first, 2 of 2)

- [Affinity-VAE: incorporating prior knowledge in representation learning from scientific images](https://mlsanity.com/paper/2209.04517/) (2022)
- [Disentangling semantic features of macromolecules in Cryo-Electron Tomography](https://mlsanity.com/paper/2106.14192/) (2021)

## Abstract (arXiv)

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.