This plugin is able to stitch a grid of images, it does not matter if it is 2D or 3D images as long as all images are of the same type. This fusion method does not work with RGB input images for obvious reasons. In the overlapping area the intensities should appear in gray scales (R + GB). Red/Cyan Overlay: In the output image the first image is colored in red, the second one colored in cyan to visualize the registration.Intensity: In the overlapping area the minimum intensity between both images is used int the output image. Intensity: In the overlapping area the maximum intensity between both images is used int the output image. The fusion alpha defines the blending function ( alpha = 0 blending by averaging, alpha = 1 linear blending, alpha > 1 non-linear blending ). Linear blending: In the overlapping area the intensity are smoothly adjusted between the two images.Average: In the overlapping area the average intensity between both images is computed.There are 5 fusion methods available right now. If the stitching was not correct increasing this number might solve it. The number of peaks defines the number of maxima in the Phase Correlation Matrix which are examined. Windowing should be always used, except the user knows well about properties of the Fourier Transform and its drawbacks. Note: If the stitching was not successful using ROIs on the obviously overlapping area might solve the problem. If the input images are RGB images the user can select which channels will be used to determine the correct overlap. They can contain rectangular ROIs which limit the search to those areas, however, the full images will be stitched together. The plugins 2D/3D Stitching take two 2D/3D images as input. Stitch Directory with Images (unknown configuration): Stitch all images that are located in a given directory without any knowledge of the tile configuration.The rough initial configuration (which image is overlapping another one) is given in tile configuration file. Stitch Collection of Images: Stitch an arbitrary number of 2D or 3D images which do not have to be in a regular grid.Stitch Image Grid Sequence: Stitch a sequence of 2D or 3D regular grids of images.Stitch Grid of Images: Stitch an arbitrary number of 2D or 3D images which are arranged in a regular grid (e.g.3D Stitching: Stitch two image stacks (3D), rectangular ROIs can be used to limit the area to search in as well.2D Stitching: Stitch two 2-dimensional images, rectangular ROIs can be used to limit the area to search in.The Stitching package comes with 4 different plugins: To remove brightness differences at the tile borders, non-linear intensity blending is applied. If more than two input images/stacks are used the correct placement of all tiles is determined using a global optimization. The 2D/3D Stitching Plugin is able to reconstruct big images/stacks from an arbitrary number of tiled input images/stacks, making use of the Fourier Shift Theorem that computes all possible translations (x, y) between two 2D/3D images at once, yielding the best overlap in terms of the cross correlation measure. The physical coordinates provided by the microscope stage are not precise enough to allow reconstruction (”Stitching”) of the whole image from individual image stacks. To overcome this drawback, motorized stages moving the sample are used to create a tiled scan of the whole specimen. Typically those specimen do not fit in the field of view of the microscope. There is an increasing demand to image large biological specimen at high resolution. Tomancak (2009) "Globally optimal stitching of tiled 3D microscopic image acquisitions", Bioinformatics, 25(11):1463-1465. If you use it successfully for your research please be so kind to cite our work: Please note that the Stitching, as well as other plugins available through Fiji, is based on a publication. 9 Stitch Multiple Series or Tile Scan File.8 Stitch Directory with Images (unknown configuration).
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