Fear, Memory, and Place: Contextual fear conditioning (CFC) is widely used as a hippocampal-dependent classical conditioning task to model human episodic memory. Lovett-Barron et al. (p. 857 ) combined in vivo imaging with pharmacology, pharmacogenetics, and optogenetics and they found that somatostatin-expressing, dendrite-targeting γ-aminobutyric acid–releasing interneurons in hippocampal area CA1 are required for CFC. During CFC, sensory features of the aversive event reach hippocampal output neurons through excitatory cortical afferents and require active inhibitory filtering to ensure that the hippocampus exclusively encodes the conditioned stimulus.

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.