A suite of tools designed to streamline immunohistochemical analysis and assess the amyloid-beta plaque environment via spatial statistics.
You can download the latest compiled, ready-to-use versions of all applications for macOS and Windows from the Releases Page.
Gain intuition about the biological meaning of a key readout from the S.A.M. tool.
- Interactive Ripley's L-Function Simulation: A tool to visualize how different glial spatial patterns (clustering, random distribution, dispersion) produce unique
L(d) - dcurves.
This suite currently includes the following tools, divided into preprocessing and analysis workflows.
- Mask Accuracy Verifier: Analyzes masks of predicted signal against raw images to flag potentially inaccurate segmentations based on intensity ratios and coverage.
- File Renamer: A batch-renaming tool to clean up filenames by removing specified parts or adding prefixes/suffixes.
- ROI Extractor: Extracts embedded ImageJ ROIs from
.tiffiles and saves them as separate.zipfiles.
- S.A.M.: Interrogates colocalization, spatial organization, and expanse of objects around amyloid-beta plaques.
- Stats Tool: Given columns in an Excel file, this tool identifies outliers using ROUT (Q=1%), determines normality, runs the appropriate statistical tests, calculates effect sizes, and optionally generates graphs.
If you use these tools in your research, please cite them as:
Walsh, SP. (2025). SAM - Spatial Analysis from Masks (Version 1.0) [Computer software]. https://doi.org/10.5281/zenodo.15851666
If you encounter a bug or have an idea for a new feature, please open a new issue. We appreciate the feedback!
The documentation in this repository is available under the MIT License.
Please Note: The S.A.M. software applications themselves are distributed under a separate, more restrictive license that is included in the download packages.