Visualization and Analysis of 3D Microscopic Images

Abstract

In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

“…Moreover, related books [4], [5] and special issues [6]- [9] include a few tutorial-style overview articles covering progress in recent years for a large variety of topics (e.g., tracking in fluorescence bioimaging [10]- [12], sub-diffraction limited imaging and single molecule localization [13], [14], parametric active contour-based image segmentation [15] ). Finally, several authors presented independently state of the art methods for specific and important topics including cell-shape analysis [16], neuron tracing [17], co-localization (percentage of co-detection of interacting protein types at the same location) [18], [19], 3D image deconvolution [20], spot detection [21] in fluorescence microscopy Even if it is generally a difficult task to present a broad view of activities in bio-image processing and analysis [2], several authors [22]- [25] already explained successfully how computer vision, image analysis and visualization algorithms combined in workflows, will play a significant role in image-based studies of cell biology.…”

Automated Identification and Measurement of Haematopoietic Stem Cells in 3D Intravital Microscopy Data

“…Image analysis is the process of extracting meaningful information from images, using manual or automated methods (the latter known as computer vision techniques) [20,21]. The selection of the appropriate image analysis method for a certain type of images determines the success rate of the analysis.…”

An open-source VAA3D plugin for real-time 3D visualization of terabyte-sized volumetric images

“…In addition to scalability, another bottleneck is the inability to efficiently explore the complicated 3D image content and thus to input user-specified information of the observed image patterns directly in the 3D space. Indeed, a number of bioimage-oriented software tools for Terabyte-scale [7,8,11] and Gigabyte-scale [12,13] images are based on 2D crosssectional views or a combined display with an arbitrary-angle cutting plane. On the other hand, the few tools supporting 3D visualization and analysis either do not scale well to the Terabyte-size [14,15], or are limited owing to high expense of licenses (e.g.…”