These are the unprocessed, raw 3D images. The tiff format images were obtained directly from the microscope; they contain the channels for the Actin and Nucleus stains together in the same folder, as well as some additional imaging meta-data. The folder of the tiff files for each cell is compressed in zip format. The fits.gz format images are in a simpler format which we used internally; they have the Actin and Nucleus channels split into separate folders.
These are our segmentations of the Actin and Nucleus images in fits.gz format. Each segmentation was manually inspected and marked as Validated or Rejected; these are sorted into separate folders.
These are triangle meshes in obj format which we generated from our segmented images. Each zip file contains five versions of the mesh, each version down-sampled by a factor from 1 to 16.
These are csv format files containing several geometric attributes for each cell that we measured computationally from the segmented images. Each file contains a row for every cell from a particular scaffold type. The attributes are described below and the equations can be found here.
For interested parties, it is possible to download multiple z-stacks
for the same scaffold type by using the wget command. For example,
the following options of the wget command can be issued when
downloading all z-stacks for the Collagen Fibril scaffold type:
wget -r -np -nH --cut-dirs=3 --no-check-certificate
A DOI has been minted for this data record: https://doi.org/doi:10.18434/M3ZP4Q
If you use this data then, please, cite the DOI and the appropriate publication: