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Tutorial. Coordinate Optimization/Generation Preliminaries: You need an updated copy of Fiji following the Stowers plugin update site. All of the plugins used This tutorial describes' how to produce an image stack (or 3D image) from an input sequence of tiles' using the Fiji plugins for stitching and registration. The Stitching Plugin (2d-5d) is able to reconstruct big images/stacks from an arbitrary number of tiled input images/stacks, making use of the Fourier Shift Image stitching using FIJI. 1. When capturing images from the SEM, make sure you save without the annotations at the bottom of the screen (e.g. scale bar). This plugin is able to stitch an arbitrary collection or grid of images, it does not matter if it is 2d, 3d, 4d or 5d images as long as all images are of the Stitching images using Fiji. 31 January 2017. Example 1 – Manual stitching with MosaicJ. 1. Go to Plugins – Stitching – MosaicJ;.In this article we will guide you through how to use Micro-Manager to acquire XY images with Scientifica's stage and use FIJI to put them together.