Year: 2025
Type: preprint
Abstract: Purpose To provide a standardized method for processing andanalyzing immunofluorescence images of mouse brain sections to quantify axonalprojections. The pipeline consists of four main stages: Cropping individualbrain sections from whole-slide scans, generating multi-channel TIFFs, warpingimages to a standard atlas for anatomical alignment, and applying a tubenessalgorithm to identify and isolate axons for quantification. ScopeThis protocol applies to .VSI files generated from scanned immunofluorescenceslides. It is designed for use with CellSense software for initial cropping andFiji (ImageJ) for all subsequent image processing and analysis. Please find an image PDF attached to help follow the protocol
Authors: Anish Singh, divya.darwinarulseeli not provided, Oscar Andres Moreno Ramos
Institution: Northwestern University
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4415112397
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