![]() Allow reordering Specifies whether layers/ sections can change their relative order in the series. We use a Tikhonov regularizer towards 1.0 weight. The per-section quality weight requires regularization to avoid trivial solutions. 0 means no regularization, 1 means full regularization (no change). Inner Regularization Specifies the amount of regularization in the outer loop of the optimizer. Inner Iterations Specifies the number of iterations in inner loops of the optimizer. The regularizer in the outer loop damps the updates during each iteration by the specified fraction. Outer regularization Specifies the amount of regularization in the outer loop of the optimizer. Outer iterations Specifies the number of iterations in the outer loop of the optimizer. Parameters Neighborhood range Specifies the neighborhood around each section for which pairwise similarities are calculated. The Fiji plugin Transform > Z-Spacing Correction and the TrakEM2 plugin Plugins > LayerZPosition implement this method. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. On summary, section thickness that is supposed to be constant, in practice is not and has to be corrected where precise measurement is desired. The software is designed for lightsheet fluorescence microscopy (LSFM, second box), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks. Optical sectioning techniques often suffer from increasing distortion as sections deeper inside the tissue are imaged. The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images (first box). The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. Serial section Microscopy, using either optical or physical sectioning, is an established method for volumetric anatomy reconstruction. Saalfeld (2015) Post-acquisition image based compensation for thickness variation in microscopy section series, In International Symposium on Biomedical Imaging (ISBI'15), New York Introduction If you use it successfully for your research please cite our work: Please note that the z-spacing correction plugin available through Fiji, is based on a publication.
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