Post-acquisition image based compensation for thickness variation in microscopy section series

Philipp Hanslovsky, John A. Bogovic, Stephan Saalfeld
11/25/2014
cs.CVq-bio.QMstat.AP

Official code: saalfeldlab/z-spacing (8 stars, GPL-2.0, last commit 2024-09-03).

Abstract

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.

View on arXivView PDF

Code Implementations(1)

saalfeldlab/z-spacingOfficial100%
GPL-2.0

Estimate the correct positions of sections of three dimensional image data.

87JavaOct 16, 20142 years agoGPL-2.0

Similar Papers

Image-Based Correction of Continuous and Discontinuous Non-Planar Axial Distortion in Serial Section Microscopy

86% match1 repo82015

Learning Multimodal Volumetric Features for Large-Scale Neuron Tracing

79% match1 repo92024

ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentation

79% match2024

Medical Image Imputation from Image Collections

78% match1 repo152018

Denoising Diffusion Probabilistic Models for Image Inpainting of Cell Distributions in the Human Brain

77% match2023

3D Segmentation of Neuronal Nuclei and Cell-Type Identification using Multi-channel Information

77% match2024

Cite this paper

@article{hanslovsky2014postacquisition,
  title  = {Post-acquisition image based compensation for thickness variation in microscopy section series},
  author = {Philipp Hanslovsky and John A. Bogovic and Stephan Saalfeld},
  year   = {2014},
  eprint = {1411.6970},
  archivePrefix = {arXiv},
  url    = {https://arxiv.org/abs/1411.6970}
}

Add a badge to your README

Shows whether official code is linked for this paper.

Code of Paper badge
[![Code of Paper](https://codeofpaper.com/badge/1411.6970.svg)](https://codeofpaper.com/paper/1411.6970)

Discussion