zebrafish-measure

Segmentation, measurement, and scale-bar calibration functions for zebrafish larvae images, factored out of the Zebrafish_webapp Gradio app so they can be shared with the SlicerZebrafishEmbryoAnalyzer 3D Slicer extension without depending on Gradio.

Install

pip install -e .

Modules

• zebrafish_measure.seg — segmentation_pipeline: runs the body/eye/edema/ swim-bladder Unet/FPN/Segformer models (downloaded from Hugging Face Hub) over a folder or list of images.
• zebrafish_measure.seg_helper — mask post-processing used by seg (hole filling, dilation, sub-pixel boundary offset) and image loading.
• zebrafish_measure.length — measurement geometry: fish body length via tube_length_border2border, eye metrics (compute_eye_metrics, compute_eye_diameters), and generic tube-shaped structure metrics (compute_tube_metrics, used for e.g. the swim bladder). Also includes the curvature classifier (FishClassifier, load_model, classification_curvature) and the standalone edge-curvature analysis (compute_curvature_profile).
• zebrafish_measure.scalebar — auto-detection and manual calibration of the image scale bar (detect_scalebar, calibrate_from_endpoints).

All public functions are re-exported from the top-level package, e.g.:

from zebrafish_measure import segmentation_pipeline, tube_length_border2border, detect_scalebar

Scope

This library intentionally excludes anything Gradio/UI-specific — that stays in Zebrafish_webapp's app.py, which depends on this package instead of containing the logic directly.