Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

Jian Mu, Lin Yang, Malgorzata Kamocka, Amy L. Zollman, Nadia Carlesso, Danny Z. Chen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

Original languageEnglish (US)
Title of host publicationProgress in Biomedical Optics and Imaging - Proceedings of SPIE
PublisherSPIE
Volume9413
ISBN (Print)9781628415032
DOIs
StatePublished - 2015
EventMedical Imaging 2015: Image Processing - Orlando, United States
Duration: Feb 24 2015Feb 26 2015

Other

OtherMedical Imaging 2015: Image Processing
CountryUnited States
CityOrlando
Period2/24/152/26/15

Fingerprint

image analysis
Image analysis
quantitative analysis
Blood Vessels
Microscopy
Microscopic examination
Bone
microscopy
bone marrow
vessels
Watersheds
cells
Chemical analysis
Bone Marrow
Image processing
notches
image processing
deletion
Three-Dimensional Imaging
Imaging techniques

Keywords

  • 3-D microscopy images
  • cell segmentation
  • quantitative analysis
  • vascular structure segmentation

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Radiology Nuclear Medicine and imaging

Cite this

Mu, J., Yang, L., Kamocka, M., Zollman, A. L., Carlesso, N., & Chen, D. Z. (2015). Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis. In Progress in Biomedical Optics and Imaging - Proceedings of SPIE (Vol. 9413). [941305] SPIE. https://doi.org/10.1117/12.2082350

Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis. / Mu, Jian; Yang, Lin; Kamocka, Malgorzata; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 9413 SPIE, 2015. 941305.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mu, J, Yang, L, Kamocka, M, Zollman, AL, Carlesso, N & Chen, DZ 2015, Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis. in Progress in Biomedical Optics and Imaging - Proceedings of SPIE. vol. 9413, 941305, SPIE, Medical Imaging 2015: Image Processing, Orlando, United States, 2/24/15. https://doi.org/10.1117/12.2082350
Mu J, Yang L, Kamocka M, Zollman AL, Carlesso N, Chen DZ. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis. In Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 9413. SPIE. 2015. 941305 https://doi.org/10.1117/12.2082350
Mu, Jian ; Yang, Lin ; Kamocka, Malgorzata ; Zollman, Amy L. ; Carlesso, Nadia ; Chen, Danny Z. / Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 9413 SPIE, 2015.
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