/Cell Tracking

Cell Tracking

Portrait of Cell Tracking
Heads: Mei Chen, Phil Campbell, Lee Weiss and Takeo Kanade
Contact: SeungIl Huh
Associated Lab: Tissue Engineering
Homepage
Last Project Publication Year: 2011

Biological engineering applies knowledge about genomics, proteomics, and cellomics to develop new diagnostics and therapeutics for medicine. The high cost and long timelines for gathering and interpreting experimental data is a barrier to efficient exploration of the complex and high-dimensional design spaces of biological-based application systems. To overcome this barrier, researchers are relying more-and-more on high-throughput micro-array technologies to simultaneously conduct hundreds to thousands of individual experiments on a single test chip. However, studying cell responses to micro-array environments (cellomics) has been limited to either single endpoint measurements or tracking a relatively few, sparsely spaced cells over time.



Based on advances in optics and imaging systems, we are developing fully-automated computer vision-based cell tracking algorithms and a web-based system that overcomes these limitations. The system tracks whole populations of cells on a test chip in real-time (i.e., image analysis be completed for each frame prior to next frame, with images typically taken at intervals of 5 to 10 minutes), not only so that results are immediately available, but so that experiments can even be modified or terminated based on real-time feedback.




Researchers can upload cell images from their database to our file server, capture microscopic images of living cells in real time and upload them, or retrieve image analysis results to check their experiment progress. Once microscopy images are uploaded to the file server, the computing clusters run cell image analysis algorithms in parallel to process images and send output results to the file server. The file server stores all image files and processed results (segmentation mask, mitosis detection, tracking trajectories and cell metrics), which can be viewed in a local graphical user interface (GUI) or through our website. Biologists can check their experiments progress conveniently (e.g. from a mobile device with internet connection), without having to wait in their lab for hours.

Displaying 20 Publications
Automated mitosis detection of stem cell populations in phase-contrast microscopy images
Seung-il Huh, D Ker, Ryoma Bise, Mei Chen and Takeo Kanade

Conference Paper, IEEE Trans. Med. Imaging, Vol. 30, No. 3, pp. 586 - 596, March, 2011
Cell Image Analysis: Algorithms, System and Applications
Takeo Kanade, Zhaozheng Yin, Ryoma Bise, SeungIl Huh, Sung Eun Eom, Michael Sandbothe and Mei Chen

Workshop Paper, IEEE Workshop on Applications of Computer Vision (WACV) 2011, January, 2011
Mitosis detection for stem cell tracking in phase-contrast microscopy images
Seung-il Huh, Sungeun Eom, Ryoma Bise, Zhaozheng Yin and Takeo Kanade

Conference Paper, IEEE International Symposium on Biomedical Imaging, pp. 2121-2127, January, 2011
Reliable Cell Tracking By Global Data Association
Ryoma Bise, Zhaozheng Yin and Takeo Kanade

Conference Paper, IEEE International Symposium on Biomedical Imaging, January, 2011
Restoring Artifact-Free Microscopy Image Sequences
Zhaozheng Yin and Takeo Kanade

Conference Paper, IEEE International Symposium on Biomedical Imaging, January, 2011
Restoring DIC Microscopy Images from Multiple Shear Directions
Zhaozheng Yin, Dai Fei Elmer Ker and Takeo Kanade

Conference Paper, IEEE International Symposium on Biomedical Imaging, January, 2011
Spatially Directed Guidance of Stem Cell Population Migration by Immobilized Patterns of Growth Factor
Eric Miller, Kang Li, Takeo Kanade, L. Walker, Lee Weiss and Philip Campbell

Journal Article, Biomaterials, Vol. 32, pp. 2775 - 2785, January, 2011
Understanding the Optics to Aid Microscopy Image Segmentation
Zhaozheng Yin, Kang Li, Takeo Kanade and Mei Chen

Conference Paper, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2010, September, 2010
Heterogeneous Conditional Random Field: Realizing Joint Detection and Segmentation of Cell Regions in Microscopic Images
Jiyan Pan, Takeo Kanade and Mei Chen

Conference Paper, IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 2010, June, 2010
Cell Segmentation in Microscopy Imagery Using a Bag of Local Bayesian Classifiers
Zhaozheng Yin, Ryoma Bise, Mei Chen and Takeo Kanade

Conference Paper, The IEEE International Symposium on Biomedical Imaging (ISBI) 2010, April, 2010
Detection of Hematopoietic Stem Cells in Microscopy Images Using a Bank of Ring Filters
Sung Eun Eom, Ryoma Bise and Takeo Kanade

Conference Paper, The IEEE International Symposium on Biomedical Imaging, April, 2010
Mitosis Sequence Detection Using Hidden Conditional Random Fields
An An Liu, K. Li and Takeo Kanade

Conference Paper, IEEE International Symposium on Biomedical Imaging (ISBI) 2010, April, 2010
Learning to Detect Different Types of Cells under Phase Contrast Microscopy
Jiyan Pan, Takeo Kanade and Mei Chen

Conference Paper, Microscopic Image Analysis with Applications in Biology (MIAAB) 2009, September, 2009
Reliably Tracking Partially Overlapping Neural Stem Cells in DIC Microscopy Image Sequences
Ryoma Bise, Kang Li, Sungeun Eom and Takeo Kanade

Workshop Paper, MICCAI Workshop on Optical Tissue Image Analysis in Microscopy, Histopathology and Endoscopy (OPTMHisE), pp. 67-77, September, 2009
Cell Population Tracking and Lineage Construction with Spatiotemporal Context
Kang Li, Mei Chen, Takeo Kanade, Eric Miller, Lee Weiss and Phil Campbell

Journal Article, Medical Image Analysis, Vol. 12, No. 5, pp. 546 - 566, October, 2008
Computer Vision Tracking of Stemness
Kang Li, Eric Miller, Mei Chen, Takeo Kanade, Lee Weiss and Phil Campbell

Conference Paper, Proc. IEEE International Symposium on Biomedical Imaging (ISBI): Special Session on In Vivo Microscopic Image Analysis, pp. 847 - 850, May, 2008
Cell Population Tracking and Lineage Construction Using Multiple-Model Dynamics Filters and Spatiotemporal Optimization
Kang Li and Takeo Kanade

Workshop Paper, Proceedings of the 2nd International Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), September, 2007
Cell Population Tracking and Lineage Construction with Spatiotemporal Context
Kang Li, Mei Chen and Takeo Kanade

Conference Paper, Proceedings of the 10th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), pp. 295 - 302, January, 2007
Online Tracking of Migrating and Proliferating Cells Imaged with Phase-Contrast Microscopy
Kang Li, Eric Miller, Lee Weiss, Phil Campbell and Takeo Kanade

Workshop Paper, Proceedings of the 2006 Conference on Computer Vision and Pattern Recognition Workshop (CVPRW '06), pp. 65 - 72, June, 2006
Tracking of Migrating and Proliferating Cells in Phase-Contrast Microscopy Imagery for Tissue Engineering
Takeo Kanade and Kang Li

Workshop Paper, Proceedings of the First International Workshop on Computer Vision for Biomedical Image Applications (CVBIA), October, 2005

Past Project People

  • Zhaozheng Yin
  • Jiyan Pan
  • Elvira Osuna-Highley
  • Eric Miller
  • An An Liu
  • Kang Li
  • Katsuya Kondo
  • Dai Fei Elmer Ker
  • Silvina Nanci Junkers
  • SeungIl Huh
  • Casey Helfrich
  • Sung Eun Eom
  • Ryoma Bise
2019-07-01T15:37:16-04:00