Data Layout

Expected structure

Provide data under data/ using this layout:

For each metadata wing_region value, matching adjacency and geometry files must exist. For example, wing_region = wd_1 maps to:

Each adjacency_matrices_<wing_region>.xlsx file contains one sheet per depth layer. Each sheet stores a square adjacency matrix:

rows and columns are cell indices (same ordering as model indices)
value 0 means no contact
value edge means the cell pair shares a contact in that layer, with shared edge length equal to edge
diagonal entries should be 0 (no self-contact)

The number of sheets should match n_layers in metadata for that region.

Each cell_geometry_<wing_region>.csv file stores cell-level geometry used by the model (for centroids, apical area, and derived diameters).

Example `cell_geometry` columns and meanings
Column	Meaning	Example
`frame`	Layer/time identifier from source segmentation (typically `0` for static inputs)	`0`
`label`	Cell index used in modelling arrays	`4`
`area`	Cell area (apical cross-section units from source data)	`1148.0`
`centroid_x`	X coordinate of cell centroid	`172.639`
`centroid_y`	Y coordinate of cell centroid	`12.360`
`original_label`	Original segmentation label before remapping	`5.0`
`perimeter`	Cell perimeter from segmentation	`85.0`
`show`	Visibility/filter flag from source preprocessing	`1.0`

data/wing_region_metadata.csv defines region-level model parameters.

Metadata columns and meaning
Column	Meaning	Example
`wing_region`	Region key used in filenames and model calls	`wd_1`
`wing_label`	Display label used in figures/legends	`1`
`gap`	Inter-layer spacing	`0.5`
`n_layers`	Number of depth layers used in simulation	`50`
`default_height`	Default SOP-band height for spacing analyses	`85`
`is_wing_disc`	Boolean selector for canonical wing-disc entries	`TRUE`
`signalling_labels`	Serialized list of signalling-capable cell indices	`[23, 25, 26, ...]`

Store signalling_labels as a JSON-like list string in each metadata row, for example "[1, 5, 9, 12]".