1. Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks
- Author
-
Klibisz, Aleksander, Rose, Derek, Eicholtz, Matthew, Blundon, Jay, and Zakharenko, Stanislav
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Quantitative Biology - Neurons and Cognition - Abstract
Calcium imaging is a technique for observing neuron activity as a series of images showing indicator fluorescence over time. Manually segmenting neurons is time-consuming, leading to research on automated calcium imaging segmentation (ACIS). We evaluated several deep learning models for ACIS on the Neurofinder competition datasets and report our best model: U-Net2DS, a fully convolutional network that operates on 2D mean summary images. U-Net2DS requires minimal domain-specific pre/post-processing and parameter adjustment, and predictions are made on full $512\times512$ images at $\approx$9K images per minute. It ranks third in the Neurofinder competition ($F_1=0.569$) and is the best model to exclusively use deep learning. We also demonstrate useful segmentations on data from outside the competition. The model's simplicity, speed, and quality results make it a practical choice for ACIS and a strong baseline for more complex models in the future., Comment: Accepted to 3rd Workshop on Deep Learning in Medical Image Analysis (http://cs.adelaide.edu.au/~dlmia3/)
- Published
- 2017