Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks

Code

• github.com/alexklibisz/deep-calcium
  OfficialIn papernone★ 0
• github.com/ankit-vaghela30/Cilia-Segmentation
  none★ 0

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 512512 images at 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.

Tasks

Reproductions