3D Cell Nuclear Morphology: Microscopy Imaging Dataset and Voxel-Based Morphometry Classification Results

Abstract

Cell deformation is regulated by complex underlying biological mechanisms associated with spatial and temporal morphological changes in the nucleus. Quantitative analysis of changes in size and shape of nuclear structures in 3D microscopic images is important not only for investigating nuclear organization, but also for detecting and treating pathological conditions such as cancer. Multiple methods have been proposed to classify cell and nuclear morphological phenotypes in 3D, however, there is a lack of publicly available 3D data for the evaluation and comparison of such algorithms. To address this problem, we present a dataset containing a of total of 1,433 segmented nuclear and 3,282 nucleolar binary masks. We also provide a baseline evaluation of a number of popular classification algorithms using voxel-based morphometric measures. Original and derived imaging data are made publicly available for downloading on the project web-page: http://www.socr.umich.edu/ projects/3d-cell-morphometry/data.html.

Hypothesis: Caco‐2 cell rotational 3D mechanogenomic turing patterns have clinical implications to colon crypts

“…Our pipeline workflow protocol may need to be tailored to each new imaging data format; however, the overall design of the protocol is not expected to drastically change. [17][18][19][20]35 Application of BAC-FISH methods to study colon crypts is feasible in our pilot study (Figure 2B). Correlating morphogenesis with oscillatory gene movement and expression including clarification of the biophysical mechanisms that determine DNA-histone interactions and their regulation by cooperative transcription factors will be required to generate convincing proof of Turing's "gene morphogenesis hypothesis" in primary cells and tissue models.…”

“…Then, the same protocol for automated cell and subnuclear structure labelling can be applied to generate solid volumetric masks of nuclear components. Our pipeline workflow protocol may need to be tailored to each new imaging data format; however, the overall design of the protocol is not expected to drastically change . Application of BAC‐FISH methods to study colon crypts is feasible in our pilot study (Figure B).…”

“…Detailed indepth description and discussion of the rotational 3D mechanogenomic Turing patterns observed during differentiation are included in the supplementary and online material ( Figure 1 and S1) (http:// www.socr.umich.edu/projects/3d-cell-morphometry/data.html). [17][18][19][20] 2 | SOME POTENTIAL APPLICATIONS OF…”

Evaluation of Methods for Cell Nuclear Structure Analysis from Microscopy Data

“…We evaluate a number of widely used classification algorithms using 2 different cross-validation schemes to assess batch effects. We demonstrate near-perfect classification performance using 2D data and compare our results with originally reported baselines [4].…”

“…In this study we use 3D Cell Nuclear Morphology Microscopy Imaging Dataset [4], one of the biggest publicly available datasets for nuclear structure classification. This dataset consists of two collections of 3D volumetric microscopic cell images with corresponding nuclear and nucleolar binary masks.…”