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Register Virtual Stack Slices

1,895 bytes added, 11:16, 6 June 2009
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<p>This plugin takes a list of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas).</p>
 <p>This howto describes the uses of the "Register Virtual Stack Slices" plugin in Fiji for the purpose of registering the slices of a stack. The registration is plugin uses any translation, rigid (translation only+rotation), or similarity (translation+rotation+translation. No isotropic scaling), no nonaffine, elastic (via bUnwarpJ with B-splines) or moving least squares transformation model, aided by automatically extracted SIFT features.</p><p><b>Premises</b>:<br /><ul><li>You have a folder with an ordered list of image files in it that ImageJ can open.</li><li>Each image represents a slice in a sequence.</li></ul></p><p>Images may have different dimensions and be of different type.</p><p><b>Step 0</b>: <a href="http://pacific.mpi-linear deformationscbg.de">Install Fiji,</a> and launch it.</p><p><b>Step 1</b>: launch the "Plugins - Registration - Register Virtual Stack Slices" plugin</p><p><b>Step 2</b>: choose the appropriate options:<br /><ul><li>The expected transformation model finding inliers (i.e. correspondences between images) in the feature extraction: translation, rigid, similarity or affine.</li><li>The image transformation model: translation, rigid, similarity, affine, elastic or moving least squares.</li><li>The process is advanced checkbox: whether to see the feature extraction parameters setup dialog, and if elastic, the bUnwarpJ dialog. Otherwise the plugin operates on reasonable, default parameters.</li></ul> </p><p><b>Step 3</b>: choose the source and target folders:<br /><ul><li>Select a source folder containing the slices, at one slice per image file.</li><li>Select the target folder where resulting registered slices are automatically stored as followstif files.</li></ul> </p><p>On success, a virtual stack will open showing all the registered images contained in the target folder. The virtual stack can be closed with no ill effect: images are saved in the target folder.</p><p>Notes:<br />
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<li>Select "Plugins - Registration - Register Virtual Stack Slices"The plugin is multithreaded: more CPU cores means faster execution.</li><li>Select whether to register with translation only (phase-correlation), or both translation and rotation (The two most relevant parameters in the SIFT).feature extraction are:<br />On choosing SIFT one can still constrain <ul><li><b>maximum image size</b>, which limits the low-end size of the registration features (i.e. decrease maximum image size to be translation-only in increase the size of the following dialogsmallest features to extract.)</li><li>If SIFT was chosen<b>inlier ratio</b>, specify algorithm parameterswhich determines when to reject the intersection set of feature correspondences between two images (ratio between correspondent features vs. all extracted features.)</li><li/ul>Select the source directory to read images from. The names must be bit-sortable.</li><li>Select All types of images are accepted (8-bit, 16-bit, 32-bit and RGB), and output images are of the target directory to store registered images tosame type as input.</li>
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