1000+ Z-stack Data Dissemination

Viewer of 3D Shapes

Original Raw Images

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.

Segmented Images

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.

Shape Measurements

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.

Batch download of z-stacks

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 https://isg.nist.gov/deepzoomweb/fileBrowsing/3D/Raw_tiff/CollagenFibril/


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:

Biomaterials: A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches.
Stephen J. Florczyk, Mylene Simon, Derek Juba, P. Scott Pine, Sumona Sarkar, Desu Chen, Paula J. Baker, Subhadip Bodhak, Mary C. Brady, Peter Bajcsy*, and Carl G. Simon, Jr.*
ACS Biomaterials Science and Engineering, August 2017, DOI: 10.1021/acsbiomaterials.7b00473
3D Segmentation: A Method for the Evaluation of Thousands of Automated 3D Stem Cell Segmentations.
Peter Bajcsy, Mylene Simon, Stephen Florczyk, Carl Simon, Derek Juba, and Mary Brady.
Journal of Microscopy, 2015 Aug 13. doi: 10.1111/jmi.12303.
Computational acceleration: Parallel Geometric Classification of Stem Cells by Their 3D Morphology.
Derek Juba, Antonio Cardone, Cheuk Yiu Ip, Carl G. Simon Jr., Christopher K. Tison, Girish Kumar, Mary Brady, and Amitabh Varshney.
Computational Science and Discovery. Volume 6, Number 1, 015007, Year 2013.
Biomaterials: Effect of the Scaffold Microenvironment on Cell Polarizability and Capacitance Determined by Probabilistic Computations.
Beatriz A. Pazmino Betancourt, Stephen J. Florczyk, Mylene Simon, Derek Juba, Jack F. Douglas, Walid Keyrouz, Peter Bajcsy, Christopher Lee and Carl G. Simon, Jr.
Biomedical Materials, BMM-101918.R1, Vol. 13, No. 2, pages 025012, Jan. 2018; URL


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Biomaterials Group