DOI: 10.5281/zenodo.17880693
title: N-Views egg geometry dataset

description: This dataset contains egg geometries, including manual measurements and photography (3D photogrammetry, monocular silhouette and N-Views methods) datasets for 6 samples of Coturnix coturnix (CC) eggs, 6 samples of Gallus gallus domesticus (GG) eggs, and microscopic digital images of two samples of the predatory mite species Amblyseius swirskii (AS).

The data is designed to validate and benchmark photography-based measurement techniques for the reconstruction of ovoid structures.

Associated Publication: https://doi.org/10.1101/2025.11.12.688065

Dataset structure

1. ImageryEggsDataset.zip

The primary imagery archive, which has the following internal structure:

./0_Photogrammetry/

Benchmarking schema for 12 egg samples reconstructed via photogrammetry (structure-from-motion).







/R_CC1/ to /R_GG6/: 12 folders each containing:



/raw_images/: 100-150 raw images (.JPG, 3456x2304 px) of an egg geometry using a turntable and fiduciary markers.

R_CC1_b.mg: Meshroom (Alicevision 2021) node graph for the structure-from-motion reconstruction pipeline.

R_CC1_b.stl: Scaled 3D output model of the egg geometry.

texture_1001.png, texturedMesh.mtl, texturedMesh.obj: Textured 3D reconstruction files.



MarkerU.pdf: Fiduciary marker used for scale/rotation.

Readme.txt: Printed marker coordinates.




./1_SilhoutteBestEffort/

Monocular top-view images for Pappus theorem reconstruction (70 mm focal length).







/calibration/: Checkerboard images (9x6, square size: 25 mm). 

/images_h/: 12 top-view images of CC and GG samples.

/masks/: Precomputed egg contours.

/out_annots/: Annotations of contours, main axis, and side lobes.

pappus_results.csv: Summary statistics for the Silhouette approach.

triad_arucomarker.pdf: Fiduciary markers in the scheme consist of the Aruco ids [0,1,2] with printed size 22 mm and separation of 7.5 mm.




./2_NViews/

Multi-view reconstruction approach for the 12 CC and GG egg samples.







/R_CC1/ to /R_GG6/: Individual sample folders containing:



/calibration/: Checkerboard images (9x6, square size: 25 mm).

/images_h/: 8 multi-view photographs.

/masks/: Precomputed egg contours.

calibration_outoput.json: Distortion and camera intrinsic matrix (OpenCV 5-parameter distortion model).

result.json: Derived output parameters for N-Views reconstruction.



triad_arucomarker.pdf: Fiduciary markers in the scheme consist of the Aruco ids [0,1,2] with printed size 22 mm and separation of 7.5 mm.




./3_NViews_ASwirskii/

Microscopic egg reconstruction for two samples of Amblyseius swirskii (AS).







/Test1_AS1_v3/

/Test1_AS2_v3/:



/calibration/: Calibration of image distortion and poses.

imagename.xlsx: Image vs. World coordinate mapping (gridded pattern 5x5, 0.05 mm squares).

calibration_results.json: Camera intrinsics and distortion.

poses.csv: Reconstructed translation/rotation vectors per image.

/images_h/: 4 multi-view photographs.

/masks/: Precomputed egg contours.

/images_annotationspose/: Estimated coordinate reference system displays.






./4_SensitivityExperiments/

Three sensitivity analyses as described in the associated publication, format structure of each replicate is analogous to ./2_NViews/R_CC1/ folder structure:







/Ex1/: Sensitivity to the camera-egg axis angle distortion (non-parallel angle theta between egg main axis and camera plane. Angles theta: [0, pi/32, pi/16, pi/8, pi/4, pi/2]). To simplify the folder naming, experiments with different angles theta are stored in folders named CC2_X and GG2_X with X: [0, 6, 11, 22, 45, 90], corresponding to the approximate angle theta in degrees) [12 samples in total].

/Ex2/: Sensitivity to image count (Exp2_1: 2 views, Exp2_2: 4 views, Exp2_3: 8 views, Exp2_4: 12 views; 10 replicates each). [40 samples in total]

/Ex3/: Focal length effects (17 mm, 50 mm, 100 mm) for CC2 and GG2 reconstructions [6 samples in total].




2. Measurements.xlsx

Ground truth and comparative data sheets across all methods (Caliper, Archimedes buoyancy displacement, photogrammetry, Silhouette, N-Views):



ComparisonMethods_samples_CC_GG: Summary of Length (mm), Diameter (mm), Volume (mm³), and SurfaceArea (mm²) across all methods (Caliper, Archimedes, Photogrammetry, N-Views, Silhouette) for all Coturnix coturnix (CC) and Gallus gallus domesticus (GG) eggs.

CaliperMeasurements_CC_GG: Manual vernier caliper measurements of length and diameter (5 independent replicates per sample).

DensityMeasurements_CC_GG: Volume via Archimedes buoyancy displacement (method described in the associated publication).