Anatolution, an online platform for consensus morphology

Abstract

IntroductionSupervised statistical learning for cell-level segmentation and morphometry in optical microscopy is limited less by algorithmic capacity than by the scarcity of reliable, expert-validated ground truth. In comparative neuroscience and quantitative histology, where classical stains such as Nissls method remain the primary means to study cellular morphology, this bottleneck is acute: manual annotation is expensive, subject to individual bias, and rarely performed at the scale or consistency that computational approaches demand. No existing platform integrates a stain-specific bioimage segmentation protocol, a structured multi-annotator workflow, and consensus-based quality control into a single pipeline from image ingestion to machine-readable training data. MethodsWe present Anatolution, an open-source, web-based platform designed to address the gap of quality annotations at https://anatolution.herokuapp.com/public-tool/. Anatolution organizes microscopy images, including 2D arrays or 3D volumes, into project workspaces where multiple annotators independently label cellular structures against a shared computer vision catalogue. This design enables systematic inter-rater and intra-rater reliability assessment, with consensus derived from agreement across annotators rather than from any single experts judgment. The platform enables the export of aggregated labels or annotation datasets for downstream statistical learning methods. We describe the systems architecture, its Nissl-specific segmentation pipeline, the consensus annotation workflow, and validation of inter-rater reliability. ConclusionAcross 20+ histological annotation containers annotated by up to 15 independent raters, consensus boundary agreement increased monotonically with annotator count, reaching a median Dice of 0.79 against the full-rater reference at seven annotators, with top-tier containers achieving leave-one-out ceiling values of 0.621-0.769 for cell-body segmentation. The segmentation pipeline provided effective spatial anchoring, with 88% of consensus-annotated polygons containing at least one algorithmically detected seed. Anatolution provides open-source infrastructure for producing consensus-validated training data from classical histological preparations, addressing the primary bottleneck limiting supervised learning for cell-level morphometry.