SACOB: Software Package Including Example Input Data

This repository contains the full software package for SACOB (Semi-Automated Counting of Buds), a modular Python-based pipeline for anatomically guided quantification of vascular bud density at the chondro-osseous border in histological sections along with an example input file for testing and demonstration purposes. The workflow combines manual annotation of the cartilage–bone interface with automated extraction of one-dimensional intensity profiles and standardized peak detection to identify vascular buds. The method enables reproducible, feature-specific quantification (buds/mm) and reduces observer-dependent variability compared to manual counting.

The software is launched via main.py, which serves as the main executable script. The src directory contains the subordinate Python modules that are called by main.py and implement the individual components of the workflow.
A sample data file is included in the data folder to enable testing of the software. The file file_list.csv contains the corresponding entry for this sample file, allowing the program to retrieve it directly from the data directory during execution.
The material provided here is intended to support transparency, reproducibility, and reuse of the software.

The repository also includes a utility script for converting multi-page TIFF microscopy images into 2D NumPy arrays via maximum-intensity projection for use with the current SACOB implementation.