Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent Markers on Coronal Brain Slices
Ben Kantor and colleagues recently published their design for Brainways, an open source software that automatically registers coronal slices and quantifies fluorescent markers. Brainways is a python based, AI registration algorithm for slice matching to the Waxholm rat
atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. Multiple channel cell detection is currently supported only through an external software import (e.g. QuPath). The Brainways automatic non-rigid
registration algorithm is based on a deep neural network architecture and is supported using the TPS interpolation registration from the Elastix python package.
To demonstrate experimental reliability, Brainways was used on an existing dataset from an experiment on the neural network involved in empathic rat behavior. The automatic analysis covered over a hundred times more brain tissue than the original manual quantification.
This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. RRID: SCR_024402
Special thanks to Lan Hooton, a neuroscience undergraduate at American University, for providing this project summary.
Access the design and code from GitHub!
Check out the repository on GitHub.
Read more about it!
Check out the pre-print to learn more!
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