Papers using CloneView

These are the manuscripts associated with the released CloneView data repositories:

Measuring Process Dynamics and Nuclear Migration for Clones of Neural Stem Cells

E. Cardenas De La Hoz, M. R. Winter, M. Apostolopoulou, S. Temple,  A.  R. Cohen, Measuring Process Dynamics and Nuclear Migration for Clones of Neural Progenitor Cells,  ECCV 2016 Workshops, Volume 9913, Springer Lecture Notes in Computer Science pp 291-305 (pdf).

Repository for adult NSC processes Repository for embryonic NSC processes
Neural stem cells (NSCs) generate processes that extend from the cell body in a  dynamic manner. The NSC nucleus migrates along these processes with patterns believed to be tightly coupled to mechanisms of cell cycle regulation and cell fate determination. Here, we describe a new segmentation and tracking approach that allows NSC processes and nuclei to be reliably tracked across multiple rounds of cell division in phase-contrast microscopy images. Results are presented for mouse adult and embryonic NSCs from hundreds of clones, or lineage trees, containing tens of thousands of cells and millions of segmentations. New visualization approaches allow the NSC nuclear and process features to be effectively visualized for an entire clone. Significant differences in process and nuclear dynamics were found among type A and type C adult NSCs, and also between embryonic NSCs cultured from the anterior and posterior cerebral cortex.
Computational Image Analysis Reveals Intrinsic Multigenerational Differences between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells

M. Winter, M. Liu, D. Monteleone, J. Melunis, U. Hershberg, S. K. Goderie, S. Temple, and A. R. Cohen, Stem Cell Reports, vol. 5, pp. 609-620, 10/13/2015,  (pubmed).

Anterior/Posterior NSC repository –

Time-lapse microscopy can capture patterns of development through multiple divisions for an entire clone of proliferating cells. Images are taken every few minutes over many days, generating data too vast to process completely by hand. Computational analysis of this data can benefit from occasional human guidance. Here we combine improved automated algorithms with minimized human validation to produce fully corrected segmentation, tracking, and lineaging results with dramatic reduction in effort. A web-based viewer provides access to data and results. The improved approach allows efficient analysis of large numbers of clones. Using this method, we studied populations of progenitor cells derived from the anterior and posterior embryonic mouse cerebral cortex, each growing in a standardized culture environment. Progenitors from the anterior cortex were smaller, less motile, and produced smaller clones compared to those from the posterior cortex, demonstrating cell-intrinsic differences that may contribute to the areal organization of the cerebral cortex.