Dataset: Optimal disk packing of chloroplasts in plant cells

This repository contains relevant information for Schramma, N., Weeks, E.R., Jalaal M. "Optimal disk packing of chloroplasts in plant cells" PNAS (2025)
All tabular files are pickle files.

Experimental data is given as tabular and  label data including chloroplast autofluorescence data: 

Analyzed label data: 

cell_shape_analysis_without_cp
contain information of measured cell shapes (label-images referred to by 'exp' column)
- contains x and y position of the label ('x','y')
- the orientation in radians
- bounding box position (in x,y)
- Perimeter [µm] and Area [µm^2]
- minor and major axes (respective the orientation) and aspect ratio. 

cell_shape_analysis_with_cp
contains additional chloroplast-related information available.
- chloroplast total area: 'CP total' [µm^2]
- mean chloroplast area 'CP mean', median chloroplast area 'CP median', standard deviation of chloroplast areas 'CP std'
- chloroplast number 'CP num'
- minimal and maximal chloroplast area 'CP min', 'CP max',
- the packing density 'packing'
- the standard deviation of chloroplast radii 'CP R std', as well as min, max, mean and median 'CP R min', 'CP R max', 'CP R mean', 'CP R median'
- experiment identifier 'exp'. All units are [µm] or [µm^2] respectively. 

Simulation data stems from disk packing simulations for random close packing in various confinement boxes (see methods in manuscript).

all_simulations_positions

For each 'number' of simulation - contains tabular data at 13.6% polydispersity.
Positions (X,Y) and radii of disks in confinement are represented relative to average diameter (d=1). 
'data'-column contains box-size information and average phi and is organized as follows:
for each 'number', the first row of 'data' is 0, the next two rows show width (Lx) and height (Ly) of simulation box.
The fifth row contains the random close packing fraction (phi). All other entries are 0.

all_simulations_summary

contains summary of simulations including
Number of particles 'N', packing fraction 'phi', width of box 'Lx' and height of box 'Ly' in units of average diameters. 

all_simulations_summary_polydisp

contains summary of all simulations with various polydispersities. Data for polydispersity 13.6% same as in all_simulations_summary. 

Image Files (.tif)

The dataset 211013 is available here: https://zenodo.org/records/6517229
Chloroplast autofluorescence imaging data:
240729_CP_glass_3_extended_depth.tif
240729_CP_glass_4_extended_depth.tif
240729_CP_glass_5_extended_depth.tif
240729_CP_glass_6_extended_depth.tif

Label images of chloroplast (result of StarDist):
240729_CP_glass_3_cp_label.tif
240729_CP_glass_4_cp_label.tif
240729_CP_glass_5_cp_label.tif
240729_CP_glass_6_cp_label.tif

Label images of cells: end with "_cell_label.tif" or "_label.tif"