Fiji/Z-Spacing Correction

Z-Spacing Correction (Fiji)
Author Philipp Hanslovsky, Stephan Saalfeld ([1])
Maintainer Philipp Hanslovsky, Stephan Saalfeld
Source [2]
Initial release April 16th, 2015
Latest version April 16th, 2015
Development status experimental, active
Category Plugins, TrakEM2, Transform


Citation

Please note that the z-spacing correction plugin available through Fiji, is based on a publication. If you use it successfully for your research please cite our work:

P. Hanslovsky, J. Bogovic, S. Saalfeld (2015) Post-acquisition image based compensation for thickness variation in microscopy section series, In International Symposium on Biomedical Imaging (ISBI'15), New York [3]

Introduction

Serial section Microscopy, using either optical or physical sectioning, is an established method for volumetric anatomy reconstruction. 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. 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. Optical sectioning techniques often suffer from increasing distortion as sections deeper inside the tissue are imaged. On summary, section thickness that is supposed to be constant, in practice is not and has to be corrected where precise measurement is desired. 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. The Fiji plugin Transform > Z-Spacing Correction and the TrakEM2 plugin Plugins > LayerZPosition implement this method.

Parameters

Neighborhood range
Specifies the neighborhood around each section for which pairwise similarities are calculated.
Outer iterations
Specifies the number of iterations in the outer loop of the optimizer.
Outer regularization
Specifies the amount of regularization in the outer loop of the optimizer. 0 means no regularization, 1 means full regularization (no change). The regularizer in the outer loop damps the updates during each iteration by the specified fraction.
Inner Iterations
Specifies the number of iterations in inner loops of the optimizer.
Inner Regularization
Specifies the amount of regularization in the outer loop of the optimizer. 0 means no regularization, 1 means full regularization (no change). The per-section quality weight requires regularization to avoid trivial solutions. We use a Tikhonov regularizer towards 1.0 weight.
Allow reordering
Specifies whether layers/ sections can change their relative order in the series.