SOCR 3D Cell Morphometry Project Data

This page contains data accompanying the paper:

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley, James E. Verdone, Robert W. Veltri, Kenneth J. Pienta, Donald S. Coffey, Brian D. Athey, Ivo D. Dinov
3D cell nuclear morphology: microscopy imaging dataset and voxel-based morphometry classification results

Usage: You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the following conditions:

  1. you agree to include a reference to the paper above when presenting or publishing your results,
  2. you agree not to re-distribute these images without inclusion of this notice.

There are two datasets in this study:

For both datasets cells were labeled with 3 different fluorophores: DAPI (4',6-diamidino-2-phenylindole) for the nuclei, while fibrillarin antibody (fibrillarin) and ethidium bromide (EtBr) were used for nucleoli staining. Original 3-channel volumes were aquired using laser scanning confocal microscope. They were then cut into 1024x1024xZ sub-volumes and channels were separated into c0, c1, and c2, correspondingly. Each link to data archive below represents one "run" of the microscope and contains original 1024x1024xZ TIFF sub-volumes in all 3 channels, as well as nuclear and nucleolar masks after segmentation and quality control. Each tarball also contains README file with detailed description of file structure inside.

The Fibroblast dataset consists of fluorescence microscope images of human fibroblast cell line. Fibroblasts (newborn male) were subjected to a G0/G1 Serum Starvation Protocol. This provided with following phenotypes: cell cycle synchronized by serum-starvation (SS) and proliferating (PROLIF). After segmentation and quality control dataset consisted of 965 nuclear masks (498 SS and 470 PROLIF) and 2,181 nucleolar masks (1,151 SS and 1,030 PROLIF).

WARNING: due to the high sparsity of images each run will take up to 20-30GB after extraction.


157 (1.25 GB)

158 (1.38 GB)

159 (1.42 GB)

163 (1.75 GB)


160 (1.43 GB)

161 (1.43 GB)

162 (1.50 GB)

164 (1.53 GB)

165 (1.25 GB)

166 (1.22 GB)

167 (1.59 GB)

The PC3 dataset consists of fluorescence microscope images of human prostate cancer cell line PC3. Slides were cultured in the phenotypic states of epithelial (EPI) and mesenchymal transition (EMT). After segmentation and quality control dataset consisted of 458 nuclear (310 EPI and 148 EMT) and 1,101 nucleolar (649 EPI and 452 EMT) masks.

NOTE: PC3 data is currently in preparation and will be uploaded in the next few weeks.