PT  - JOURNAL ARTICLE
AU  - Li Zhou
AU  - Chao Yang
AU  - Weiguo Gao
AU  - Talita Perciano
AU  - Karen M. Davies
AU  - Nicholas K. Sauter
TI  - Subcellular structure segmentation from cryo-electron tomograms via machine learning
AID  - 10.1101/2020.04.09.034025
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.09.034025
4099  - http://biorxiv.org/content/early/2020/04/09/2020.04.09.034025.short
4100  - http://biorxiv.org/content/early/2020/04/09/2020.04.09.034025.full
AB  - We describe how to use several machine learning techniques organized in a learning pipeline to segment and identify subcellular structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging techniques that try to piece together disconnected components that should belong to the same subcellular structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here work well for extracting membrane surfaces of protein reconstituted liposomes in a cellular environment that contains other artifacts.