Applications for whole-brain recordings
A napari plug-in.
Uses: automated and curated segmentation and time series extraction of GCaMP volumetric recordings, optionally with NeuroPAL, of immobilized worms. Eats-worm is a full data-processing pipeline that takes in raw recordings and metadata, does pre-processing, finds neuron centers, assigns probabilistic labels to neurons, and extracts time series calcium activity from those neurons.
This software is written and managed by the Foundations of Cognition Lab. Instructions for installation and use of eats-worm is provided on the readme page of the github repository. Open-source.
Standalone app for MacOS and Windows.
Uses: visualization, annotation, neuronal segmentation and identification, neural tracking, activity trace extraction and stimulus presentation data of volumetric NeuroPAL images, optionally with whole-brain activity.Now updated with functionality for histogram matching, color-corrected image visualization, and automated neural identification using the new Statistical Atlas.
This software is written and managed by the Yemini Lab; further information can be found on the Yemini lab website. A tutorial for using this app can be found here. Open-source.
Do you have relevant software / data tools to share?
Please contact us and if suitable, we would be love to include your tools into this community resource.