Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks

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 512×512 images at $\approx9Kimagesperminute.ItranksthirdintheNeurofindercompetition(F_1=0.569$) 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/)