STAGETOOL-Online_v1.0.0_interface-spec_and_examples

STAGETOOL Online v1.0.0: interface specification and example tiles This archive documents STAGETOOL Online v1.0.0, a public web service for automated analysis of mouse spermatogenesis. STAGETOOL Online performs deep-learning–based staging of seminiferous tubules and classification of epithelial cell types from DAPI-stained mouse testis cross-sections. The deployed models and weights are identical to those described in the original STAGETOOL publication (Endocrinology, 2022); no retraining was performed for this release. Contents Interface specification (PDF): input requirements, expected outputs, privacy/retention policy, and versioning. Example input tiles: representative 1024×1024 px, ×400, DAPI-stained mouse seminiferous tubule cross-sections. Corresponding outputs: tubule instance masks with stage labels, per-cell class labels, and tabular summaries. Online service (current deployment) Service URL: https://stagetool.utu.fi Accepted inputs: single-tile TIFF/PNG/JPEG images at 1024×1024 px, acquired at ×400 magnification. Retention: uploaded images are deleted within 24 h. Validation & preprocessing: non-1024×1024 inputs are rejected; 8- and 16-bit grayscale and color TIFFs are supported; all inputs are internally converted to contiguous 3-channel uint8 BGR arrays for inference. Runtime: public-site inference is CPU-based, typically < 1 min per 1024×1024 tile. Scope and limitations Whole-testis / whole-slide analyses, protein or gene expression overlays, and knockout model characterization are available on request through collaboration.Intended use: research use on mouse material only. This service is not for clinical or diagnostic purposes. How to cite Please cite: Meikar et al., “STAGETOOL, a Novel Automated Approach for Mouse Testis Histological Analysis,” Endocrinology (2022). The accompanying Application Note describing STAGETOOL Online (this submission / Zenodo record). Files This record contains an interface specification PDF plus example inputs/outputs in separate folders.