6 research outputs found
Post-acquisition image based compensation for thickness variation in microscopy section series
Serial section Microscopy 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.
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.
First experiments show promising results on both serial section Transmission
Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron
Microscopy (FIB-SEM) series. We made our solution available as Open Source
plugins for the TrakEM2 software and the ImageJ distribution Fiji
Estimation of sample spacing in stochastic processes
Motivated by applications in electron microscopy, we study the situation where a stationary and isotropic random field is observed on two parallel planes with unknown distance. We propose an estimator for this distance. Under the tractable, yet flexible class of Lévy-based random field models, we derive an approximate variance of the estimator. The estimator and the approximate variance perform well in two simulation studies