Quantification of Axonal Projections from Whole-Brain Slide Images
Output Details
Description
Purpose
To provide a standardized method for processing and analyzing immunofluorescence images of mouse brain sections to quantify axonal projections. The pipeline consists of four main stages: Cropping individual brain sections from whole-slide scans, generating multi-channel TIFFs, warping images to a standard atlas for anatomical alignment, and applying a tubeness algorithm to identify and isolate axons for quantification.
Scope
This protocol applies to .VSI files generated from scanned immunofluorescence slides. It is designed for use with CellSense software for initial cropping and Fiji (ImageJ) for all subsequent image processing and analysis.
Identifier (DOI)
10.17504/protocols.io.6qpvrwrjplmk/v1
