SOCR 3D Cell Morphometry Project Data

http://www.socr.umich.edu/projects/3d-cell-morphometry/data.html

There are 2 datasets in this project:

  1. Fibroblast and PC3 cell imaging data [1, 2, 3].
    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.

  2. Caco-2 cell imaging data [4].
    Cells were labeled with 4 different fluorophores: DAPI (4',6-diamidino-2-phenylindole) for the nuclei, HES1 Alexa 647 (1:200; Abcam), NR3C1 Alexa 488 (1:150; Cell signaling) and OCLN Alexa 594 (1:600; Thermo Fisher). Original multichannel volumes were aquired using laser scanning confocal microscope. For protocol details see [4]. Images were saved in Analyze image format, in which each 3D image is represented by a pair of files: .img and .hdr.

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 corresponding paper when presenting or publishing your results,
  2. you agree not to re-distribute these images without inclusion of this notice.

Please cite corresponding papers if you use these data:

  1. 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
    2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, Salt Lake City, UT, June 18-22, 2018, pp. 2272-2280. [link]

  2. Alexandr A. Kalinin, Brian D. Athey, Ivo D. Dinov
    Evaluation of Methods for Cell Nuclear Structure Analysis from Microscopy Data
    7th International Conference on Analysis of Images, Social Networks and Texts (AIST-SUP 2018), Moscow, Russia, July 5-7, 2018. [preprint]

  3. Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, 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 Shape Modeling for Cell Nuclear Morphological Analysis and Classification
    Under review. [preprint]

  4. Gen Zheng, Alexandr A. Kalinin, Ivo D. Dinov, Walter Meixner, Shengtao Zhu, John Wiley
    Hypothesis: Caco-2 cell rotational 3D mechanogenomic Turing patterns has clinical implications to colon crypts
    Journal of Cellular and Molecular Medicine (in press) [preprint]


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: each run will take up to 20-30GB after extraction.

PROLIF:

157 (1.25 GB)

158 (1.38 GB)

159 (1.42 GB)

163 (1.75 GB)

SS:

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.


The Caco2 dataset consists of 103 3D fluorescence microscope images of human colon cancer cell line Caco-2.

WARNING: Full dataset takes ~120GB after unpacking.

NOTE: Any 3D image in either Nifti and Analyze formats can be viewed interactively in web-browser using SOCR BrainViewer web-app. To use BrainViewer, drag and drop an image (.nii.gz or .img+.hdr) into a browser window or press 'Select files' button. Use controls to switch between 2D and 3D views.

Single image in Nifti format (2 MB)

Sample images in Nifti format (243 MB)

Full dataset in Analyze format (14 GB)