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. 2011:182-186.
doi: 10.1109/isbi.2011.5872383.

A CURVICYLINDRICAL COORDINATE SYSTEM FOR THE VISUALIZATION AND SEGMENTATION OF THE ASCIDIAN TAIL

Golnaz Abdollahian  1 , Michael Veeman, William Smith, B S Manjunath
Affiliations

A CURVICYLINDRICAL COORDINATE SYSTEM FOR THE VISUALIZATION AND SEGMENTATION OF THE ASCIDIAN TAIL

Golnaz Abdollahian et al. Proc IEEE Int Symp Biomed Imaging. 2011.

Abstract

State of the art biological imaging methods, such as confocal microscopy, create 3D volumes by sampling on a cartesian grid. This cartesian coordinate system is often not convenient for visualization and analysis of multi layered organs or tissues. The ascidian embryonic tail, for example, is organized along anterioposterior (AP), dorsoventral (DV) and left-right (LR) axes that are locally orthogonal but curved in the XYZ microscope space. Here, we propose a "curvicylindrical" coordinate system for analysis of such biological structures. By extracting representative paths that traverse different tissue layers, the embryo can be visualized in a small number of 2D images (3 images in the case of the ascidian tail). As we demonstrate, this reduction of the dimensionality from 3D to 2D facilitates the initialization process for high quality segmentation of different cell types, and identification of tissue boundaries.

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Figures

Fig. 1
Fig. 1
An example of a confocal image of an ascidian embryo tail. (A) the maximum intensity projection of the stack, (B) a lateral section (XY) and a cross section (XZ) view, and (C) a pseudo-colored cross section showing different cell types.
Fig. 2
Fig. 2
(a) The curvicylindrical coordinate system with respect to part of an ascidian tail; (b) sampling planes, which are orthogonal to the AP axis.
Fig. 3
Fig. 3
Sampling contours for the three tissue layers in an ascidian embryo, from left to right: notochord, muscle and skin layers.
Fig. 4
Fig. 4
The unwrapped tissue layers of ascidian embryo tail: (a)notochord, (b) muscle-neural tube-gut, and (c) skin.
Fig. 5
Fig. 5
Initialization is done using the 2D tissue images as in (a), (b) and (c). The obtained seed points are converted back into the original coordinates for segmentation as shown in (d).
Fig. 6
Fig. 6
Segmentation results for notochord cells (left) and muscle cells (right).
Fig. 7
Fig. 7
3D rendering of segmented muscle and notochord cells at four different stages.
Fig. 8
Fig. 8
Using Fast Marching to find the tissue boundaries, which are parallel to the θ axis in the curvicylindrical coordinate system.
Fig. 9
Fig. 9
Non-rigid registration of the the tail points (left) into a semi cylindrical model (right).
Fig. 10
Fig. 10
Results of the skin layer detection (left: original cross sections, and right: result of skin layer detection and removal.
See this image and copyright information in PMC

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