Finally, because it produces a single 2D image with no need of an interactive interface. Second, because resolution is always lower in z than in x/ y in fluorescence microscopes. First, because it contains the highest amount of information. In this case, a projection in the z direction is often preferred. In contrast, a 3D stack contains all pieces of information needed to reconstruct a focused 2D image. This is because at high resolution, those objects cannot hold within the depth of field of a microscope and therefore a single 2D image acquisition often suffers from being only partially in focus. Image stacks are also useful to image flattish or so-called 2.5D objects such as an epithelium, a monolayered cell culture, a membrane within an in vivo tissue sample or a flat biological structure such as cultured neurons. A variety of software programme as Voxx 6, NIH’s Fiji/ImageJ 7 or VTK 8 propose such options with an interactive visualization. Optionally, a detection step can be introduced before the projection to focus on the reconstruction of layers of interest 5. In this case, a single projection cannot be satisfactory and an interactive rendering tool must be used to obtain successive projections of the data in arbitrary directions using transparency filters. Unlike a single 2D image, which can be rendered and interpreted straightforwardly on a screen, a 3D stack needs to be processed to be displayed.Īn image stack can be employed to image a full 3D object. Furthermore, it is common nowadays to image the same preparation repetitively at various depths to obtain a three-dimensional (3D) image under the form of a stack of two-dimensional (2D) images. Cell biologists routinely use fluorescence microscopy to observe spatial organization of organelles, co-localization of vesicles or to study the impact of gene expression or small compounds on cell morphology 1, 2, 3, 4.

Convert 3d image into 2d matlab