  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.
