Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks

Aleksander Klibisz, Derek C. Rose, Matthew Eicholtz, Jay Blundon, Stanislav Zakharenko

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 \(512\,\times \,512\) images at \(\approx \)9K images per minute. It ranks third in the Neurofinder competition (\(F_1=0.57\)) 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.