TABLE 1.

Metashape processes, parameters, settings and rationales.

Process	Parameter	Setting	Rationale (if applicable)
Align photos	Accuracy	Highest	Prevents downscaling of images for feature point selection
	Generic Preselection	On	Default. Reduction of computation time for feature matching as initial feature mapping performed on down‐sampled images
	Reference Preselection	Estimated	Default. Reduction of computation time for photo alignment, uses estimated exterior orientation parameters
	Key Point Limit	40,000	Recommended by Metashape
	Tie Point Limit	4000	Recommended by Metashape
	Exclude Stationary Tie Points	On	Supresses lens artefacts
	Guided image matching	Off	Default
	Adaptive camera model fitting	Off	Default
Build dense cloud
	Quality	Ultra high	Prevents downscaling of original images
	Depth filtering	Aggressive	Reduces excessive noise and artefacts in the dense cloud
	Reuse depths maps	On	Reduces computation time for subsequent runs
	Calculate point colors	On	Required for colour rendering of models
	Calculate point confidence	Off	Parameter can be used for dense cloud filtering but this is not applied as filtering is done during the Build Mesh process
Build mesh	Source Data	Depth Maps	Less resource intensive than generating from dense cloud.
	Surface type	Arbitrary (3D)	Biological specimens are non‐planar
	Quality	Ultra high	Prevents downscaling during meshing. Uses original captured photographic information
	Face count	High	Creates mesh with the highest possible faces, allows more detail in the representation of complex surfaces
	Interpolation	Enabled	Default, automatically fills holes in model
	Depth filtering	Aggressive	Setting reduced wet specimen artefacts during empirical testing
	Calculate vertex colors	On	Required for colour rending of models
	Reuse depth maps	On	Reduces computation time for subsequent runs
Build texture	Texture Type	Diffuse Map	Default. Applies photographic texture map rather than geometric normal map or occlusion map
	Source data	Images	Using original captured colour information
	Mapping mode	Keep uv	Default. Reduces computation time for subsequent runs
	Blending mode	Mosaic	Default
	Texture size/count	16,384 × 1	Creates textures at 16 K resolution. Down‐sampling can be completed later if required.
	Enable hole filling	On	Creates a smooth surface impression
	Enable ghosting filter	On	Creates a smooth surface impression
	Transfer texture	Off	Default
Decimate texture	Face count	500,000	Increases computer performance when viewing models