This paper is a revision of a paper presented at the SPIE conference on Medical Imaging 2005: Physiology, Function, and Structure from Medical Images, Feb. 2005, San Diego, California. The paper presented there appears (unrefereed) in SPIE Proceedings Vol. 5746.
Segmentation, or separating an image into distinct objects, is the key to creating 3-D renderings from serial slice images. This is typically a manual process requiring trained persons to tediously outline and isolate the objects in each image. We describe a template-based semiautomatic segmentation method to aid in the segmentation process and 3-D reconstruction of microscopic objects recorded with a confocal laser scanning microscope (CLSM). The simple and robust algorithm is based on the creation of a user-defined object template, followed by automatic segmentation of the object in each of the remaining image slices. The user guides the process by selecting the initial image slice for the object template, and labeling the object of interest. The algorithm is applied to mathematically defined shapes to verify the performance of the software. The algorithm is then applied to biological samples, including neurons in the common housefly. It is the quest to further understand the visual system of the housefly that provides the opportunity to develop this segmentation algorithm. Further application of this algorithm may extend to other registered and aligned serial section datasets with high contrast objects.
Our understanding of the world around us is based primarily on three-dimensional information because of the environment in which we live and interact. Medical or biological image information is often collected in the form of two-dimensional, serial section images. As such, it is difficult for the observer to mentally reconstruct the three dimensional features of each object. Although many image rendering software packages allow for 3D views of the serial sections, they lack the ability to segment, or isolate different objects in the data set. Segmentation is the key to creating 3D renderings of distinct objects from serial slice images, like separate pieces to a puzzle. This paper describes a segmentation method for objects recorded with serial section images. The user defines threshold levels and object labels on a single image of the data set that are subsequently used to automatically segment each object in the remaining images of the same data set, while maintaining boundaries between contacting objects. The performance of the algorithm is verified using mathematically defined shapes. It is then applied to the visual neurons of the housefly, Musca domestica. Knowledge of the fly’s visual system may lead to improved machine visions systems. This effort has provided the impetus to develop this segmentation algorithm. The described segmentation method can be applied to any high contrast serial slice data set that is well aligned and registered. The medical field alone has many applications for rapid generation of 3D segmented models from MRI and other medical imaging modalities.
Two challenges to an effective, real-world computer vision system are speed and reliable object recognition. Traditional computer vision sensors such as CCD arrays take considerable time to transfer all the pixel values for each image frame to a processing unit. One way to bypass this bottleneck is to design a sensor front-end which uses a biologically-inspired analog, parallel design that offers preprocessing and adaptive circuitry that can produce edge maps in real-time. This biomimetic sensor is based on the eye of the common house fly (Musca domestica). Additionally, this sensor has demonstrated an impressive ability to detect objects at subpixel resolution. However, the format of the image information provided by such a sensor is not a traditional bitmap transfer of the image format and, therefore, requires novel computational manipulations to make best use of this sensor output. The real-world object recognition challenge is being addressed by using a subspace method which uses eigenspace object models created from multiple reference object appearances. In past work, the authors have successfully demonstrated image object recognition techniques for surveillance images of various military targets using such eigenspace appearance representations. This work, which was later extended to partially occluded objects, can be generalized to a wide variety of object recognition applications. The technique is based upon a large body of eigenspace research described elsewhere. Briefly described, the technique creates target models by collecting a set of target images and finding a set of eigenvectors that span the target image space. Once the eigenvectors are found, an eigenspace model (also called a subspace model) of the target is generated by projecting target images on to the eigenspace. New images to be recognized are then projected on to the eigenspace for object recognition. For occluded objects, we project the image on to reduced dimensional subspaces of the original eigenspace (i.e., a “subspace of a subspace” or a “sub-eigenspace”). We then measure how close a match we can achieve when the occluded target image is projected on to a given sub-eigenspace. We have found that this technique can result in significantly improved recognition of occluded objects. In order to manage the combinatorial “explosion” associated with selecting the number of subspaces required and then projecting images on to those sub-eigenspaces for measurement, we use a variation on the A* (called “A-star”) search method. The challenge of tying these two subsystems (the biomimetic sensor and the subspace object recognition module) together into a coherent and robust system is formidable. It requires specialized computational image and signal processing techniques that will be described in this paper, along with preliminary results. The authors believe that this approach will result in a fast, robust computer vision system suitable for the non-ideal real-world environment.
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