SCAMP - an open-source tool for the quantification of calcification in fish larvae

Abstract

Quantifying skeletal mineralization phenotypes in larval fish is complicated by the natural curvature of the notochord and by sample-to-sample variability in orientation, staining and imaging. Consequently, many studies rely on summary measures such as vertebral counts or total stain intensity. Here we present SCAMP (Spinal Calcification & Mineralization Profiler), an open-source, GUI-based Python tool that computationally straightens the curved notochord of Alizarin Red S-stained fish larvae and generates standardized mineralization profiles along the spinal axis. This approach reduces positional and shape variability, allowing direct, quantitative comparison of calcification patterns within and between experimental cohorts, without requiring programming expertise. We validate SCAMP using a zebrafish model of Pseudoxanthoma elasticum (abcc6aelu15/elu15), recovering genotype-specific differences in the intensity, extent and spatial distribution of ectopic calcification. Using SCAMP, we further show that inorganic pyrophosphate (PPi) supplementation of the medium suppresses ectopic notochord calcification, alters the anterior-posterior distribution of mineralized regions in homozygous mutants, and promotes mineralization at physiological vertebral sites. We also show that methylene blue, a routine antifungal additive in fish medium, reduces baseline calcification, with the most pronounced effects observed in heterozygous controls. SCAMP is freely available and has the potential to be adapted to other fish species used in skeletal and mineralization research.

Plant phenotyping relevance

魚類幼生の石灰化表現型を画像から定量化するオープンソース解析ツールを開発・検証しており、表現型取得・抽出法が研究の中心である。

Code and data availability

The supplied blocks describe the SCAMP tool and zebrafish calcification analysis, but contain no authors' public repository URL, deposit, or availability link for the SCAMP code, image data, or analysis outputs. The only URL mentioned (Pillow docs) is a generic library, not a paper-specific asset.

No evidence-backed public reproduction asset is currently recorded.