Quantification of Axonal Projections from Whole-Brain Slide Images v1
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 Kumar Singh (ORCID: https://orcid.org/0000-0002-9749-7994)
- Oscar A. Ramos
- divya.darwinarulseeli not provided (ORCID: https://orcid.org/0000-0003-0268-1500)
Publication Details
- Published
- 2025-09-30
- DOI
- https://doi.org/10.17504/protocols.io.6qpvrwrjplmk/v1
- Primary Topic
- Medical Imaging and Analysis
- Type
- article
- Field-Weighted Citation Impact
- 0.00