Cell-Scaffold Contact Z-stack Data Dissemination

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Original Raw Images After Cropping Based on Verified Cell Segmentation

These are the unprocessed, raw 3D images after cropping. The files were converted from a sequence of tiff format images (obtained directly from the microscope) to a single fits format file for a simpler download. The z-stack fits format files of cell membrane channel have a file name notation ch00 while the z-stack files of scaffold channel have a file name notation ch01.

Segmented Cells

These are files of binary masks for segmented cells in fits.zip file format after cropping. Each segmentation was manually inspected using the web verification system available from the project web page.

Cell-Scaffold Contacts from Geometrical Model

These are files of binary masks for cell-scaffold contacts in fits format obtained by applying the planar (spun coat) and cylindrical (fibers) geometrical models to scaffolds.

Cell-Scaffold Contacts from Statistical Model

These are files of binary masks of cell-scaffold contacts in fits format obtained by applying the mixed pixel statistical model to scaffolds.

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 one set of raw z-stacks (cells, scaffolds) for the Spun Coat 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/M3V01R

If you use this data then, please, cite the DOI and the appropriate publication:

Automated High-Quality Cell-Scaffold Contact Measurements: Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte-sized Images.
Peter Bajcsy, Soweon Yoon, Stephen Florczyk, Nathan Hotaling, Mylene Simon, Piotr Szczypinski, Nicholas Schaub, Carl Simon Jr., Mary Brady, and Ram Sriram
BMC Bioinformatics, November 2017, 18:526, DOI 10.1186/s12859-017-1928-x; URL


ITL-Software and Systems Division
Information Systems Group
MML-Biosystems and Biomaterials Division
Biomaterials Group
Technical University of Lodz,Poland-Institute of Electronics,